universiti putra malaysia genetic diversity analysis …psasir.upm.edu.my/id/eprint/76089/1/ita 2014...
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UNIVERSITI PUTRA MALAYSIA
GENETIC DIVERSITY ANALYSIS OF COLOURED UPLAND RICE GERMPLASM USING SSR MARKERS QUANTITATIVE TRAITS AND
NUTRITIONAL QUALITY
FAIZ AHMAD
ITA 2014 7
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GENETIC DIVERSITY ANALYSIS OF COLOURED UPLAND RICEGERMPLASM USING SSR MARKERS QUANTITATIVE TRAITS AND
NUTRITIONAL QUALITY
By
FAIZ AHMAD
Thesis Submitted to the School of Graduate StudiesUniversiti Putra Malaysia in Fulfilment of the
Requirement for the Degree of Master of Science
April 2014
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COPYRIGHT
All material contained within the thesis including without limitation text logosicons photographs and all other artwork is copyright material of Universiti PutraMalaysia unless otherwise stated Use may be made of any material containedwithin the thesis for non-commercial purposes from the copyright holderCommercial use of material may only be made with the express prior writtenpermission of Universiti Putra Malaysia
Copyright copy Universiti Putra Malaysia
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DEDICATION
THIS THESIS IS SPECIALLY DEDICATED
TO
MY PARENTS MY BELOVED FAMILY AND FRIENDS
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Abstractof thesis presented to the Senate of Universiti Putra Malaysia in fulfillment ofthe requirement for the Degree of Master of Science
GENETIC DIVERSITY ANALYSIS OF COLOURED UPLAND RICEGERMPLASM REVEALED BY SSR MARKER QUANTITATIVE TRAITS
AND NUTRITIONAL QUALITY
By
FAIZ AHMAD
April 2014
Chairman Professor Mohamed Hanafi Musa PhD
Institute Tropical Agriculture
Rice (Oryza sativa L) is a staple food for many people around the world It containshigh carbohydrate which is as a source of energy Currently people are more concernabout healthy food intake Coloured rice is one of the alternatives for healthy dietbecause it has high nutritional value In addition coloured rice have antioxidantscompound such as polyphenols carotenoids and tocochromanols These antioxidantshave significant important health effect in human body In this study 42 selectedcoloured upland rice accessions were obtained from International Rice ResearchInstitute (IRRI) There were collected from difference places around the world Toreveal the genetic diversity among the accessions 25 short sequence repeated (SSR)markers were used in this study Out of 25 SSR markers used in this study only 21were polymorphic The polymorphic information content (PIC) value ranged from 0(RM 338 RM 431 RM 118 RM 133) to 0760 (RM 455) Mean of expectedheterozygosity (He) was 0470 and Shannonrsquos information index ranged from 0380 to1660 From SSR markers clustering analysis using JaccardSimiliarity Coefficientshowed that all the accessions were clustered into 7 groups The seeds among allaccessions were planted in the glasshouse for multiplication morphological andassessments of agronomical characteristic using randomized complete block design(RCBD) with 3 replications for each accession The following parameters werecollected number of tiller per plant number of panicle per plant plant height lengthflag leaf panicle length percentage of filled grain percentage of unfilled grain harvestindex yield per plant 100 grains weight days to flowering days to maturity length
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breath ratio of kernel kernel length chlorophyll content (SPAD reading) at 40 and 60days All data were analyzed by using SAS 92 software Agro-morphologicalcharacters showed significant variation among all accessions The heritability from 25agro-morphological characters and nutrient content (macro amp micro) in rice strawranged from 5652 to 9931 The nutrient contents (macro amp micro) in rice grainvaried greatly among accessions The antioxidant activities for all rice accessionsdetermined by 11- Diphenyl-2-picrylhydazyl (DPPH) radical scavenging effect methodranges from 3185 to 9845 Based on the content of vitamin E (tocochromanols) thetocotrienol content was higher than that of tocopherol for all accessions selected Theselection of better rice accessions for future breeding program could be obtained usinginformation from agro-morphological data and nutritional status of the rice accessions
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Abstraktesis yang dikemukakankepadakepadaSenatUniversiti Putra Malaysia sebagaimemenuhi keperluan untuk ijazah Master Sains
ANALISIS KEPELBAGAIAN GENETIK DALAM JANAPLASMA PADI BUKITBERWARNA MENGGUNAKAN PENANDA SSR TRAIT KUANTITATIF DAN
KUALITI NUTRISI
Oleh
FAIZ AHMAD
April 2014
Pengerusi Professor Mohamed Hanafi Musa PhD
InstitutPertanianTropika
Padi (Oryza sativa L) adalah makanan ruji pada kebanyakan orang di seluruh dunia Iamempunyai kandungan karbohidrat yang tinggi iaitu salah satu daripada sumbertenaga Belakangan ini masyarakat lebih prihatin terhadap pengambilan makananberkhasiatPadi berwarna adalah salah satu alternative untuk diet berkhasiat keranamempunyai kandungan nutrisi yang tinggi Di samping itu padi berwarna mempunyaikomponen antioksida seperti ldquopolyphenolsrdquo ldquocarotenoidsrdquo dan ldquotocochromanolsrdquoKomponen antioksida ini mempunyai kepentingan yang signifikan kepada kesihatantubuh manusia Dalam kajian ini sebanyak 42 aksesi padi bukit bewarna diperolehi dariInstitut Penyelidikan Padi Antarabangsa (IRRI) Ia terdiri daripada koleksi pelbagaitempat dari seluruh dunia Untuk mendedahkan kepelbagaian genetic antara aksesi 25penanda SSR telah digunakan dalam kajian ini Daripada 25 penanda SSR digunakandalam kajian ini hanya 21 yang polimorfik Min He adalah 0470 dan indeks informasiShannons adalah antara julat daripada 0380 sehingga 1660 Daripada penanda SSRanalisis kluster menggunakan ldquoJaccardSimiliarity Coefficientrdquo menunjukkan kesemuaaksesi telah diklusterkan sebanyak 7 kumpulan Biji benih antara aksesi telah ditanamdi rumah kaca untuk multiplikasi ciri-ciri penilaian morfologi dan agronomimenggunakan model RCBD dengan 3 replikasi bagi setiap aksesi Parameter tersebuttelah dikumpulkanbilanganbatang per pokok bilangan tangkai per pokok tinggipokok panjang daun bendera panjang tangkai buah terisi per tangkai buah tak terisiper tangkai indeks tuaian hasil per pokok 100 berat buah hari untuk berbunga hari
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untuk matang nisbah panjang lebar biji panjang biji kandungan klorofil (bacaan spad)pada 40 dan 60 hari Kesemua data ini telah dianalisi smenggunakan perisian SAS 92Ciri-cirimorfologi dan agronomi menunjukkan signifikasi pada variasi antara semuaaksesi Keterwarisan daripada 25 ciri-ciri agro-morfologi dan kandungan nutrisi(makroampmikro) dalam jerami pad antara julat dari 5652 sehingga 9931 Kandungannutrisi (makroampmikro) dalam biji padi amat berbeza antara aksesi Aktiviti antioksidauntuk kesemua aksesi padi ditentukan oleh kaedah radika memerangkap 11- Diphenyl-2-picrylhydazyl (DPPH) antara jula tdari 3185 sehingga 9845 Berdasarkankandungan vitamin E (tocochromanols) kandungan ldquotocotrienolrdquo adalah tinggi daripadaldquotocopherolrdquo bagi semua aksesi Pemilihan untuk aksesi beras yang lebih baik untukprogram pembiakbakaan boleh dibuat menggunakan maklumat daripada agro-morfologidan status nutrisi aksesi
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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Bergman CJ and Xu Z (2003) Genotype and environment effects on the tocolsand gamma-oryzanol contents of Southern US rice Cereal Chemistry 80446-449
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Butsat S and Siriamornpun S (2010) Antioxidant capacities and phenoliccompounds of the husk bran and endosperm of Thai rice Food Chemistry119 606-613
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Chun L Mi J G Li F Chen F Zhang F (2005) Genetic analysis of maize rootcharacteristics in response to low nitrogen stress Plant and Soil 369-382
Claudia AP Torres LB Jose CR Alfredo IL Enrique D Sunethra E MarkLuis HE (2008) Phosphate availability alters lateral root development inArabidopsis by modulating auxin sensitivity via mechanism involving theTIR1 auxin receptor Plant Cell 203258-3272
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Fasahat P Muhammad K Abdullah A Ratnam W (2012) Proximatenutritional composition and antioxidant properties of Oryza rufipogon a
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wild rice collected from Malaysia compared to cultivated rice MR 219Australian Journal of Crop Science 6 1502-1507
FinocchiaroF Ferrari B GianinettiA AstaCD Galaverna G ScazzinaFPellegrini N (2007) Characterization of antioxidant compounds of red andwhite rice and changes in total antioxidant capacity during processingMolecular Nutrition and Food Research 51(2007) 1006 ndash 1019
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Frei M and Becker K (2003) Studies on the in vitro starch digestibility and theglycemic index of six different indigenous rice cultivars from thePhilippines Food Chemistry 83 395-402
Fuentes JL Cornide MT Alvarez ASuarez E Borges E (2005) Geneticdiversity analysis of rice varieties (Oryza sativa L) based on morphologicalpedigree and DNA polymorphism data Plant Genetics Resources 3 353-359
Gahoonia TS amp Nielsen NE (2004) Root traits as tools for creating phosphorusefficient varieties Plant and Soil 260 47-57
El-Gammal MI and Shakour AA (2001) Emission of pollutant from harvest andburning of rice straw in Egypt villages (North East of Nile Delta) Journal ofUnion of Arab Biologist 15 191-206
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GENETIC DIVERSITY ANALYSIS OF COLOURED UPLAND RICEGERMPLASM USING SSR MARKERS QUANTITATIVE TRAITS AND
NUTRITIONAL QUALITY
By
FAIZ AHMAD
Thesis Submitted to the School of Graduate StudiesUniversiti Putra Malaysia in Fulfilment of the
Requirement for the Degree of Master of Science
April 2014
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COPYRIGHT
All material contained within the thesis including without limitation text logosicons photographs and all other artwork is copyright material of Universiti PutraMalaysia unless otherwise stated Use may be made of any material containedwithin the thesis for non-commercial purposes from the copyright holderCommercial use of material may only be made with the express prior writtenpermission of Universiti Putra Malaysia
Copyright copy Universiti Putra Malaysia
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DEDICATION
THIS THESIS IS SPECIALLY DEDICATED
TO
MY PARENTS MY BELOVED FAMILY AND FRIENDS
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Abstractof thesis presented to the Senate of Universiti Putra Malaysia in fulfillment ofthe requirement for the Degree of Master of Science
GENETIC DIVERSITY ANALYSIS OF COLOURED UPLAND RICEGERMPLASM REVEALED BY SSR MARKER QUANTITATIVE TRAITS
AND NUTRITIONAL QUALITY
By
FAIZ AHMAD
April 2014
Chairman Professor Mohamed Hanafi Musa PhD
Institute Tropical Agriculture
Rice (Oryza sativa L) is a staple food for many people around the world It containshigh carbohydrate which is as a source of energy Currently people are more concernabout healthy food intake Coloured rice is one of the alternatives for healthy dietbecause it has high nutritional value In addition coloured rice have antioxidantscompound such as polyphenols carotenoids and tocochromanols These antioxidantshave significant important health effect in human body In this study 42 selectedcoloured upland rice accessions were obtained from International Rice ResearchInstitute (IRRI) There were collected from difference places around the world Toreveal the genetic diversity among the accessions 25 short sequence repeated (SSR)markers were used in this study Out of 25 SSR markers used in this study only 21were polymorphic The polymorphic information content (PIC) value ranged from 0(RM 338 RM 431 RM 118 RM 133) to 0760 (RM 455) Mean of expectedheterozygosity (He) was 0470 and Shannonrsquos information index ranged from 0380 to1660 From SSR markers clustering analysis using JaccardSimiliarity Coefficientshowed that all the accessions were clustered into 7 groups The seeds among allaccessions were planted in the glasshouse for multiplication morphological andassessments of agronomical characteristic using randomized complete block design(RCBD) with 3 replications for each accession The following parameters werecollected number of tiller per plant number of panicle per plant plant height lengthflag leaf panicle length percentage of filled grain percentage of unfilled grain harvestindex yield per plant 100 grains weight days to flowering days to maturity length
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breath ratio of kernel kernel length chlorophyll content (SPAD reading) at 40 and 60days All data were analyzed by using SAS 92 software Agro-morphologicalcharacters showed significant variation among all accessions The heritability from 25agro-morphological characters and nutrient content (macro amp micro) in rice strawranged from 5652 to 9931 The nutrient contents (macro amp micro) in rice grainvaried greatly among accessions The antioxidant activities for all rice accessionsdetermined by 11- Diphenyl-2-picrylhydazyl (DPPH) radical scavenging effect methodranges from 3185 to 9845 Based on the content of vitamin E (tocochromanols) thetocotrienol content was higher than that of tocopherol for all accessions selected Theselection of better rice accessions for future breeding program could be obtained usinginformation from agro-morphological data and nutritional status of the rice accessions
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Abstraktesis yang dikemukakankepadakepadaSenatUniversiti Putra Malaysia sebagaimemenuhi keperluan untuk ijazah Master Sains
ANALISIS KEPELBAGAIAN GENETIK DALAM JANAPLASMA PADI BUKITBERWARNA MENGGUNAKAN PENANDA SSR TRAIT KUANTITATIF DAN
KUALITI NUTRISI
Oleh
FAIZ AHMAD
April 2014
Pengerusi Professor Mohamed Hanafi Musa PhD
InstitutPertanianTropika
Padi (Oryza sativa L) adalah makanan ruji pada kebanyakan orang di seluruh dunia Iamempunyai kandungan karbohidrat yang tinggi iaitu salah satu daripada sumbertenaga Belakangan ini masyarakat lebih prihatin terhadap pengambilan makananberkhasiatPadi berwarna adalah salah satu alternative untuk diet berkhasiat keranamempunyai kandungan nutrisi yang tinggi Di samping itu padi berwarna mempunyaikomponen antioksida seperti ldquopolyphenolsrdquo ldquocarotenoidsrdquo dan ldquotocochromanolsrdquoKomponen antioksida ini mempunyai kepentingan yang signifikan kepada kesihatantubuh manusia Dalam kajian ini sebanyak 42 aksesi padi bukit bewarna diperolehi dariInstitut Penyelidikan Padi Antarabangsa (IRRI) Ia terdiri daripada koleksi pelbagaitempat dari seluruh dunia Untuk mendedahkan kepelbagaian genetic antara aksesi 25penanda SSR telah digunakan dalam kajian ini Daripada 25 penanda SSR digunakandalam kajian ini hanya 21 yang polimorfik Min He adalah 0470 dan indeks informasiShannons adalah antara julat daripada 0380 sehingga 1660 Daripada penanda SSRanalisis kluster menggunakan ldquoJaccardSimiliarity Coefficientrdquo menunjukkan kesemuaaksesi telah diklusterkan sebanyak 7 kumpulan Biji benih antara aksesi telah ditanamdi rumah kaca untuk multiplikasi ciri-ciri penilaian morfologi dan agronomimenggunakan model RCBD dengan 3 replikasi bagi setiap aksesi Parameter tersebuttelah dikumpulkanbilanganbatang per pokok bilangan tangkai per pokok tinggipokok panjang daun bendera panjang tangkai buah terisi per tangkai buah tak terisiper tangkai indeks tuaian hasil per pokok 100 berat buah hari untuk berbunga hari
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untuk matang nisbah panjang lebar biji panjang biji kandungan klorofil (bacaan spad)pada 40 dan 60 hari Kesemua data ini telah dianalisi smenggunakan perisian SAS 92Ciri-cirimorfologi dan agronomi menunjukkan signifikasi pada variasi antara semuaaksesi Keterwarisan daripada 25 ciri-ciri agro-morfologi dan kandungan nutrisi(makroampmikro) dalam jerami pad antara julat dari 5652 sehingga 9931 Kandungannutrisi (makroampmikro) dalam biji padi amat berbeza antara aksesi Aktiviti antioksidauntuk kesemua aksesi padi ditentukan oleh kaedah radika memerangkap 11- Diphenyl-2-picrylhydazyl (DPPH) antara jula tdari 3185 sehingga 9845 Berdasarkankandungan vitamin E (tocochromanols) kandungan ldquotocotrienolrdquo adalah tinggi daripadaldquotocopherolrdquo bagi semua aksesi Pemilihan untuk aksesi beras yang lebih baik untukprogram pembiakbakaan boleh dibuat menggunakan maklumat daripada agro-morfologidan status nutrisi aksesi
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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viii
This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
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Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
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COPYRIGHT
All material contained within the thesis including without limitation text logosicons photographs and all other artwork is copyright material of Universiti PutraMalaysia unless otherwise stated Use may be made of any material containedwithin the thesis for non-commercial purposes from the copyright holderCommercial use of material may only be made with the express prior writtenpermission of Universiti Putra Malaysia
Copyright copy Universiti Putra Malaysia
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DEDICATION
THIS THESIS IS SPECIALLY DEDICATED
TO
MY PARENTS MY BELOVED FAMILY AND FRIENDS
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Abstractof thesis presented to the Senate of Universiti Putra Malaysia in fulfillment ofthe requirement for the Degree of Master of Science
GENETIC DIVERSITY ANALYSIS OF COLOURED UPLAND RICEGERMPLASM REVEALED BY SSR MARKER QUANTITATIVE TRAITS
AND NUTRITIONAL QUALITY
By
FAIZ AHMAD
April 2014
Chairman Professor Mohamed Hanafi Musa PhD
Institute Tropical Agriculture
Rice (Oryza sativa L) is a staple food for many people around the world It containshigh carbohydrate which is as a source of energy Currently people are more concernabout healthy food intake Coloured rice is one of the alternatives for healthy dietbecause it has high nutritional value In addition coloured rice have antioxidantscompound such as polyphenols carotenoids and tocochromanols These antioxidantshave significant important health effect in human body In this study 42 selectedcoloured upland rice accessions were obtained from International Rice ResearchInstitute (IRRI) There were collected from difference places around the world Toreveal the genetic diversity among the accessions 25 short sequence repeated (SSR)markers were used in this study Out of 25 SSR markers used in this study only 21were polymorphic The polymorphic information content (PIC) value ranged from 0(RM 338 RM 431 RM 118 RM 133) to 0760 (RM 455) Mean of expectedheterozygosity (He) was 0470 and Shannonrsquos information index ranged from 0380 to1660 From SSR markers clustering analysis using JaccardSimiliarity Coefficientshowed that all the accessions were clustered into 7 groups The seeds among allaccessions were planted in the glasshouse for multiplication morphological andassessments of agronomical characteristic using randomized complete block design(RCBD) with 3 replications for each accession The following parameters werecollected number of tiller per plant number of panicle per plant plant height lengthflag leaf panicle length percentage of filled grain percentage of unfilled grain harvestindex yield per plant 100 grains weight days to flowering days to maturity length
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breath ratio of kernel kernel length chlorophyll content (SPAD reading) at 40 and 60days All data were analyzed by using SAS 92 software Agro-morphologicalcharacters showed significant variation among all accessions The heritability from 25agro-morphological characters and nutrient content (macro amp micro) in rice strawranged from 5652 to 9931 The nutrient contents (macro amp micro) in rice grainvaried greatly among accessions The antioxidant activities for all rice accessionsdetermined by 11- Diphenyl-2-picrylhydazyl (DPPH) radical scavenging effect methodranges from 3185 to 9845 Based on the content of vitamin E (tocochromanols) thetocotrienol content was higher than that of tocopherol for all accessions selected Theselection of better rice accessions for future breeding program could be obtained usinginformation from agro-morphological data and nutritional status of the rice accessions
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Abstraktesis yang dikemukakankepadakepadaSenatUniversiti Putra Malaysia sebagaimemenuhi keperluan untuk ijazah Master Sains
ANALISIS KEPELBAGAIAN GENETIK DALAM JANAPLASMA PADI BUKITBERWARNA MENGGUNAKAN PENANDA SSR TRAIT KUANTITATIF DAN
KUALITI NUTRISI
Oleh
FAIZ AHMAD
April 2014
Pengerusi Professor Mohamed Hanafi Musa PhD
InstitutPertanianTropika
Padi (Oryza sativa L) adalah makanan ruji pada kebanyakan orang di seluruh dunia Iamempunyai kandungan karbohidrat yang tinggi iaitu salah satu daripada sumbertenaga Belakangan ini masyarakat lebih prihatin terhadap pengambilan makananberkhasiatPadi berwarna adalah salah satu alternative untuk diet berkhasiat keranamempunyai kandungan nutrisi yang tinggi Di samping itu padi berwarna mempunyaikomponen antioksida seperti ldquopolyphenolsrdquo ldquocarotenoidsrdquo dan ldquotocochromanolsrdquoKomponen antioksida ini mempunyai kepentingan yang signifikan kepada kesihatantubuh manusia Dalam kajian ini sebanyak 42 aksesi padi bukit bewarna diperolehi dariInstitut Penyelidikan Padi Antarabangsa (IRRI) Ia terdiri daripada koleksi pelbagaitempat dari seluruh dunia Untuk mendedahkan kepelbagaian genetic antara aksesi 25penanda SSR telah digunakan dalam kajian ini Daripada 25 penanda SSR digunakandalam kajian ini hanya 21 yang polimorfik Min He adalah 0470 dan indeks informasiShannons adalah antara julat daripada 0380 sehingga 1660 Daripada penanda SSRanalisis kluster menggunakan ldquoJaccardSimiliarity Coefficientrdquo menunjukkan kesemuaaksesi telah diklusterkan sebanyak 7 kumpulan Biji benih antara aksesi telah ditanamdi rumah kaca untuk multiplikasi ciri-ciri penilaian morfologi dan agronomimenggunakan model RCBD dengan 3 replikasi bagi setiap aksesi Parameter tersebuttelah dikumpulkanbilanganbatang per pokok bilangan tangkai per pokok tinggipokok panjang daun bendera panjang tangkai buah terisi per tangkai buah tak terisiper tangkai indeks tuaian hasil per pokok 100 berat buah hari untuk berbunga hari
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untuk matang nisbah panjang lebar biji panjang biji kandungan klorofil (bacaan spad)pada 40 dan 60 hari Kesemua data ini telah dianalisi smenggunakan perisian SAS 92Ciri-cirimorfologi dan agronomi menunjukkan signifikasi pada variasi antara semuaaksesi Keterwarisan daripada 25 ciri-ciri agro-morfologi dan kandungan nutrisi(makroampmikro) dalam jerami pad antara julat dari 5652 sehingga 9931 Kandungannutrisi (makroampmikro) dalam biji padi amat berbeza antara aksesi Aktiviti antioksidauntuk kesemua aksesi padi ditentukan oleh kaedah radika memerangkap 11- Diphenyl-2-picrylhydazyl (DPPH) antara jula tdari 3185 sehingga 9845 Berdasarkankandungan vitamin E (tocochromanols) kandungan ldquotocotrienolrdquo adalah tinggi daripadaldquotocopherolrdquo bagi semua aksesi Pemilihan untuk aksesi beras yang lebih baik untukprogram pembiakbakaan boleh dibuat menggunakan maklumat daripada agro-morfologidan status nutrisi aksesi
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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xvi
53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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xvii
LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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2
There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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88
REFERENCES
Abdullah A ItoS Adhana K(2006) Estimate of Rice Consumption In AsianCountries and the World Towards 2050 Proceedings for Workshop andConference on Rice in the World at Stake 2 School Lunch Programs andRice Consumption Behaviors International Comparison pp 28-43
Ahn SW Bonman JM Brandon DM Groth DE Gunnel PS Hibino HHollier CA Lee FN Mew TW Prot JC Rush MC SchneiderRW Webster RK Whitney G (1992) In Compendium of Rice DiseasesAPS press
Allard RW (1960) Principles of Plant Breeding John Whiley Sons Inc NewYork pp 485
Ali SS Jafri SJH Khan TZ Mahmood A Butt MA (2000)Heritability ofyield and yield components of rice Pakistan Journal of AgriculturalResearch 16 89-91
Angela H GraziellaB Claude D Francisco M Martin C (2009) Plant rootgrowth architecture and function Plant Soil 321 153-187
Bainton SJ Plumb VE Juliano BO Perez CM Roxas DB Khush GSJesus JC Gomez KA (1991) Variation in the nutritional of rice strawAnimal Feed Science and Technology 34 261-277
Barker R(1986) Setting priorities for rice research in West Africa Paper presentedat the seminar of the International Rice Research Institute Los BanosAugust 1986
Bergman CJ and Xu Z (2003) Genotype and environment effects on the tocolsand gamma-oryzanol contents of Southern US rice Cereal Chemistry 80446-449
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DEDICATION
THIS THESIS IS SPECIALLY DEDICATED
TO
MY PARENTS MY BELOVED FAMILY AND FRIENDS
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Abstractof thesis presented to the Senate of Universiti Putra Malaysia in fulfillment ofthe requirement for the Degree of Master of Science
GENETIC DIVERSITY ANALYSIS OF COLOURED UPLAND RICEGERMPLASM REVEALED BY SSR MARKER QUANTITATIVE TRAITS
AND NUTRITIONAL QUALITY
By
FAIZ AHMAD
April 2014
Chairman Professor Mohamed Hanafi Musa PhD
Institute Tropical Agriculture
Rice (Oryza sativa L) is a staple food for many people around the world It containshigh carbohydrate which is as a source of energy Currently people are more concernabout healthy food intake Coloured rice is one of the alternatives for healthy dietbecause it has high nutritional value In addition coloured rice have antioxidantscompound such as polyphenols carotenoids and tocochromanols These antioxidantshave significant important health effect in human body In this study 42 selectedcoloured upland rice accessions were obtained from International Rice ResearchInstitute (IRRI) There were collected from difference places around the world Toreveal the genetic diversity among the accessions 25 short sequence repeated (SSR)markers were used in this study Out of 25 SSR markers used in this study only 21were polymorphic The polymorphic information content (PIC) value ranged from 0(RM 338 RM 431 RM 118 RM 133) to 0760 (RM 455) Mean of expectedheterozygosity (He) was 0470 and Shannonrsquos information index ranged from 0380 to1660 From SSR markers clustering analysis using JaccardSimiliarity Coefficientshowed that all the accessions were clustered into 7 groups The seeds among allaccessions were planted in the glasshouse for multiplication morphological andassessments of agronomical characteristic using randomized complete block design(RCBD) with 3 replications for each accession The following parameters werecollected number of tiller per plant number of panicle per plant plant height lengthflag leaf panicle length percentage of filled grain percentage of unfilled grain harvestindex yield per plant 100 grains weight days to flowering days to maturity length
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breath ratio of kernel kernel length chlorophyll content (SPAD reading) at 40 and 60days All data were analyzed by using SAS 92 software Agro-morphologicalcharacters showed significant variation among all accessions The heritability from 25agro-morphological characters and nutrient content (macro amp micro) in rice strawranged from 5652 to 9931 The nutrient contents (macro amp micro) in rice grainvaried greatly among accessions The antioxidant activities for all rice accessionsdetermined by 11- Diphenyl-2-picrylhydazyl (DPPH) radical scavenging effect methodranges from 3185 to 9845 Based on the content of vitamin E (tocochromanols) thetocotrienol content was higher than that of tocopherol for all accessions selected Theselection of better rice accessions for future breeding program could be obtained usinginformation from agro-morphological data and nutritional status of the rice accessions
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Abstraktesis yang dikemukakankepadakepadaSenatUniversiti Putra Malaysia sebagaimemenuhi keperluan untuk ijazah Master Sains
ANALISIS KEPELBAGAIAN GENETIK DALAM JANAPLASMA PADI BUKITBERWARNA MENGGUNAKAN PENANDA SSR TRAIT KUANTITATIF DAN
KUALITI NUTRISI
Oleh
FAIZ AHMAD
April 2014
Pengerusi Professor Mohamed Hanafi Musa PhD
InstitutPertanianTropika
Padi (Oryza sativa L) adalah makanan ruji pada kebanyakan orang di seluruh dunia Iamempunyai kandungan karbohidrat yang tinggi iaitu salah satu daripada sumbertenaga Belakangan ini masyarakat lebih prihatin terhadap pengambilan makananberkhasiatPadi berwarna adalah salah satu alternative untuk diet berkhasiat keranamempunyai kandungan nutrisi yang tinggi Di samping itu padi berwarna mempunyaikomponen antioksida seperti ldquopolyphenolsrdquo ldquocarotenoidsrdquo dan ldquotocochromanolsrdquoKomponen antioksida ini mempunyai kepentingan yang signifikan kepada kesihatantubuh manusia Dalam kajian ini sebanyak 42 aksesi padi bukit bewarna diperolehi dariInstitut Penyelidikan Padi Antarabangsa (IRRI) Ia terdiri daripada koleksi pelbagaitempat dari seluruh dunia Untuk mendedahkan kepelbagaian genetic antara aksesi 25penanda SSR telah digunakan dalam kajian ini Daripada 25 penanda SSR digunakandalam kajian ini hanya 21 yang polimorfik Min He adalah 0470 dan indeks informasiShannons adalah antara julat daripada 0380 sehingga 1660 Daripada penanda SSRanalisis kluster menggunakan ldquoJaccardSimiliarity Coefficientrdquo menunjukkan kesemuaaksesi telah diklusterkan sebanyak 7 kumpulan Biji benih antara aksesi telah ditanamdi rumah kaca untuk multiplikasi ciri-ciri penilaian morfologi dan agronomimenggunakan model RCBD dengan 3 replikasi bagi setiap aksesi Parameter tersebuttelah dikumpulkanbilanganbatang per pokok bilangan tangkai per pokok tinggipokok panjang daun bendera panjang tangkai buah terisi per tangkai buah tak terisiper tangkai indeks tuaian hasil per pokok 100 berat buah hari untuk berbunga hari
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untuk matang nisbah panjang lebar biji panjang biji kandungan klorofil (bacaan spad)pada 40 dan 60 hari Kesemua data ini telah dianalisi smenggunakan perisian SAS 92Ciri-cirimorfologi dan agronomi menunjukkan signifikasi pada variasi antara semuaaksesi Keterwarisan daripada 25 ciri-ciri agro-morfologi dan kandungan nutrisi(makroampmikro) dalam jerami pad antara julat dari 5652 sehingga 9931 Kandungannutrisi (makroampmikro) dalam biji padi amat berbeza antara aksesi Aktiviti antioksidauntuk kesemua aksesi padi ditentukan oleh kaedah radika memerangkap 11- Diphenyl-2-picrylhydazyl (DPPH) antara jula tdari 3185 sehingga 9845 Berdasarkankandungan vitamin E (tocochromanols) kandungan ldquotocotrienolrdquo adalah tinggi daripadaldquotocopherolrdquo bagi semua aksesi Pemilihan untuk aksesi beras yang lebih baik untukprogram pembiakbakaan boleh dibuat menggunakan maklumat daripada agro-morfologidan status nutrisi aksesi
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
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Abstractof thesis presented to the Senate of Universiti Putra Malaysia in fulfillment ofthe requirement for the Degree of Master of Science
GENETIC DIVERSITY ANALYSIS OF COLOURED UPLAND RICEGERMPLASM REVEALED BY SSR MARKER QUANTITATIVE TRAITS
AND NUTRITIONAL QUALITY
By
FAIZ AHMAD
April 2014
Chairman Professor Mohamed Hanafi Musa PhD
Institute Tropical Agriculture
Rice (Oryza sativa L) is a staple food for many people around the world It containshigh carbohydrate which is as a source of energy Currently people are more concernabout healthy food intake Coloured rice is one of the alternatives for healthy dietbecause it has high nutritional value In addition coloured rice have antioxidantscompound such as polyphenols carotenoids and tocochromanols These antioxidantshave significant important health effect in human body In this study 42 selectedcoloured upland rice accessions were obtained from International Rice ResearchInstitute (IRRI) There were collected from difference places around the world Toreveal the genetic diversity among the accessions 25 short sequence repeated (SSR)markers were used in this study Out of 25 SSR markers used in this study only 21were polymorphic The polymorphic information content (PIC) value ranged from 0(RM 338 RM 431 RM 118 RM 133) to 0760 (RM 455) Mean of expectedheterozygosity (He) was 0470 and Shannonrsquos information index ranged from 0380 to1660 From SSR markers clustering analysis using JaccardSimiliarity Coefficientshowed that all the accessions were clustered into 7 groups The seeds among allaccessions were planted in the glasshouse for multiplication morphological andassessments of agronomical characteristic using randomized complete block design(RCBD) with 3 replications for each accession The following parameters werecollected number of tiller per plant number of panicle per plant plant height lengthflag leaf panicle length percentage of filled grain percentage of unfilled grain harvestindex yield per plant 100 grains weight days to flowering days to maturity length
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breath ratio of kernel kernel length chlorophyll content (SPAD reading) at 40 and 60days All data were analyzed by using SAS 92 software Agro-morphologicalcharacters showed significant variation among all accessions The heritability from 25agro-morphological characters and nutrient content (macro amp micro) in rice strawranged from 5652 to 9931 The nutrient contents (macro amp micro) in rice grainvaried greatly among accessions The antioxidant activities for all rice accessionsdetermined by 11- Diphenyl-2-picrylhydazyl (DPPH) radical scavenging effect methodranges from 3185 to 9845 Based on the content of vitamin E (tocochromanols) thetocotrienol content was higher than that of tocopherol for all accessions selected Theselection of better rice accessions for future breeding program could be obtained usinginformation from agro-morphological data and nutritional status of the rice accessions
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Abstraktesis yang dikemukakankepadakepadaSenatUniversiti Putra Malaysia sebagaimemenuhi keperluan untuk ijazah Master Sains
ANALISIS KEPELBAGAIAN GENETIK DALAM JANAPLASMA PADI BUKITBERWARNA MENGGUNAKAN PENANDA SSR TRAIT KUANTITATIF DAN
KUALITI NUTRISI
Oleh
FAIZ AHMAD
April 2014
Pengerusi Professor Mohamed Hanafi Musa PhD
InstitutPertanianTropika
Padi (Oryza sativa L) adalah makanan ruji pada kebanyakan orang di seluruh dunia Iamempunyai kandungan karbohidrat yang tinggi iaitu salah satu daripada sumbertenaga Belakangan ini masyarakat lebih prihatin terhadap pengambilan makananberkhasiatPadi berwarna adalah salah satu alternative untuk diet berkhasiat keranamempunyai kandungan nutrisi yang tinggi Di samping itu padi berwarna mempunyaikomponen antioksida seperti ldquopolyphenolsrdquo ldquocarotenoidsrdquo dan ldquotocochromanolsrdquoKomponen antioksida ini mempunyai kepentingan yang signifikan kepada kesihatantubuh manusia Dalam kajian ini sebanyak 42 aksesi padi bukit bewarna diperolehi dariInstitut Penyelidikan Padi Antarabangsa (IRRI) Ia terdiri daripada koleksi pelbagaitempat dari seluruh dunia Untuk mendedahkan kepelbagaian genetic antara aksesi 25penanda SSR telah digunakan dalam kajian ini Daripada 25 penanda SSR digunakandalam kajian ini hanya 21 yang polimorfik Min He adalah 0470 dan indeks informasiShannons adalah antara julat daripada 0380 sehingga 1660 Daripada penanda SSRanalisis kluster menggunakan ldquoJaccardSimiliarity Coefficientrdquo menunjukkan kesemuaaksesi telah diklusterkan sebanyak 7 kumpulan Biji benih antara aksesi telah ditanamdi rumah kaca untuk multiplikasi ciri-ciri penilaian morfologi dan agronomimenggunakan model RCBD dengan 3 replikasi bagi setiap aksesi Parameter tersebuttelah dikumpulkanbilanganbatang per pokok bilangan tangkai per pokok tinggipokok panjang daun bendera panjang tangkai buah terisi per tangkai buah tak terisiper tangkai indeks tuaian hasil per pokok 100 berat buah hari untuk berbunga hari
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untuk matang nisbah panjang lebar biji panjang biji kandungan klorofil (bacaan spad)pada 40 dan 60 hari Kesemua data ini telah dianalisi smenggunakan perisian SAS 92Ciri-cirimorfologi dan agronomi menunjukkan signifikasi pada variasi antara semuaaksesi Keterwarisan daripada 25 ciri-ciri agro-morfologi dan kandungan nutrisi(makroampmikro) dalam jerami pad antara julat dari 5652 sehingga 9931 Kandungannutrisi (makroampmikro) dalam biji padi amat berbeza antara aksesi Aktiviti antioksidauntuk kesemua aksesi padi ditentukan oleh kaedah radika memerangkap 11- Diphenyl-2-picrylhydazyl (DPPH) antara jula tdari 3185 sehingga 9845 Berdasarkankandungan vitamin E (tocochromanols) kandungan ldquotocotrienolrdquo adalah tinggi daripadaldquotocopherolrdquo bagi semua aksesi Pemilihan untuk aksesi beras yang lebih baik untukprogram pembiakbakaan boleh dibuat menggunakan maklumat daripada agro-morfologidan status nutrisi aksesi
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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xvii
LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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1
CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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breath ratio of kernel kernel length chlorophyll content (SPAD reading) at 40 and 60days All data were analyzed by using SAS 92 software Agro-morphologicalcharacters showed significant variation among all accessions The heritability from 25agro-morphological characters and nutrient content (macro amp micro) in rice strawranged from 5652 to 9931 The nutrient contents (macro amp micro) in rice grainvaried greatly among accessions The antioxidant activities for all rice accessionsdetermined by 11- Diphenyl-2-picrylhydazyl (DPPH) radical scavenging effect methodranges from 3185 to 9845 Based on the content of vitamin E (tocochromanols) thetocotrienol content was higher than that of tocopherol for all accessions selected Theselection of better rice accessions for future breeding program could be obtained usinginformation from agro-morphological data and nutritional status of the rice accessions
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Abstraktesis yang dikemukakankepadakepadaSenatUniversiti Putra Malaysia sebagaimemenuhi keperluan untuk ijazah Master Sains
ANALISIS KEPELBAGAIAN GENETIK DALAM JANAPLASMA PADI BUKITBERWARNA MENGGUNAKAN PENANDA SSR TRAIT KUANTITATIF DAN
KUALITI NUTRISI
Oleh
FAIZ AHMAD
April 2014
Pengerusi Professor Mohamed Hanafi Musa PhD
InstitutPertanianTropika
Padi (Oryza sativa L) adalah makanan ruji pada kebanyakan orang di seluruh dunia Iamempunyai kandungan karbohidrat yang tinggi iaitu salah satu daripada sumbertenaga Belakangan ini masyarakat lebih prihatin terhadap pengambilan makananberkhasiatPadi berwarna adalah salah satu alternative untuk diet berkhasiat keranamempunyai kandungan nutrisi yang tinggi Di samping itu padi berwarna mempunyaikomponen antioksida seperti ldquopolyphenolsrdquo ldquocarotenoidsrdquo dan ldquotocochromanolsrdquoKomponen antioksida ini mempunyai kepentingan yang signifikan kepada kesihatantubuh manusia Dalam kajian ini sebanyak 42 aksesi padi bukit bewarna diperolehi dariInstitut Penyelidikan Padi Antarabangsa (IRRI) Ia terdiri daripada koleksi pelbagaitempat dari seluruh dunia Untuk mendedahkan kepelbagaian genetic antara aksesi 25penanda SSR telah digunakan dalam kajian ini Daripada 25 penanda SSR digunakandalam kajian ini hanya 21 yang polimorfik Min He adalah 0470 dan indeks informasiShannons adalah antara julat daripada 0380 sehingga 1660 Daripada penanda SSRanalisis kluster menggunakan ldquoJaccardSimiliarity Coefficientrdquo menunjukkan kesemuaaksesi telah diklusterkan sebanyak 7 kumpulan Biji benih antara aksesi telah ditanamdi rumah kaca untuk multiplikasi ciri-ciri penilaian morfologi dan agronomimenggunakan model RCBD dengan 3 replikasi bagi setiap aksesi Parameter tersebuttelah dikumpulkanbilanganbatang per pokok bilangan tangkai per pokok tinggipokok panjang daun bendera panjang tangkai buah terisi per tangkai buah tak terisiper tangkai indeks tuaian hasil per pokok 100 berat buah hari untuk berbunga hari
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untuk matang nisbah panjang lebar biji panjang biji kandungan klorofil (bacaan spad)pada 40 dan 60 hari Kesemua data ini telah dianalisi smenggunakan perisian SAS 92Ciri-cirimorfologi dan agronomi menunjukkan signifikasi pada variasi antara semuaaksesi Keterwarisan daripada 25 ciri-ciri agro-morfologi dan kandungan nutrisi(makroampmikro) dalam jerami pad antara julat dari 5652 sehingga 9931 Kandungannutrisi (makroampmikro) dalam biji padi amat berbeza antara aksesi Aktiviti antioksidauntuk kesemua aksesi padi ditentukan oleh kaedah radika memerangkap 11- Diphenyl-2-picrylhydazyl (DPPH) antara jula tdari 3185 sehingga 9845 Berdasarkankandungan vitamin E (tocochromanols) kandungan ldquotocotrienolrdquo adalah tinggi daripadaldquotocopherolrdquo bagi semua aksesi Pemilihan untuk aksesi beras yang lebih baik untukprogram pembiakbakaan boleh dibuat menggunakan maklumat daripada agro-morfologidan status nutrisi aksesi
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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Kang HW Cho YG Yoon UH Eun MY (1998) A Rapid DNA Extractionmethod for RFLP and PCR Analysis from a Single Dry Seed PlantMolecular Biology Reporter 161-9
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Lehmann J Martin HL Lashley EL Marshall MW Judd JT (1986)Vitamin E in foods from high and low linoleic acid diets Journal ofAmerican Dietetic Association 86 1208-1216
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Linkohr BI Williamson LC Fitter AH Leyser O (2002) Nitrate andphosphate availability and distribution have different effects on root systemarchitecture of Arabidopsis Plant Journal 29751-760
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Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
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Abstraktesis yang dikemukakankepadakepadaSenatUniversiti Putra Malaysia sebagaimemenuhi keperluan untuk ijazah Master Sains
ANALISIS KEPELBAGAIAN GENETIK DALAM JANAPLASMA PADI BUKITBERWARNA MENGGUNAKAN PENANDA SSR TRAIT KUANTITATIF DAN
KUALITI NUTRISI
Oleh
FAIZ AHMAD
April 2014
Pengerusi Professor Mohamed Hanafi Musa PhD
InstitutPertanianTropika
Padi (Oryza sativa L) adalah makanan ruji pada kebanyakan orang di seluruh dunia Iamempunyai kandungan karbohidrat yang tinggi iaitu salah satu daripada sumbertenaga Belakangan ini masyarakat lebih prihatin terhadap pengambilan makananberkhasiatPadi berwarna adalah salah satu alternative untuk diet berkhasiat keranamempunyai kandungan nutrisi yang tinggi Di samping itu padi berwarna mempunyaikomponen antioksida seperti ldquopolyphenolsrdquo ldquocarotenoidsrdquo dan ldquotocochromanolsrdquoKomponen antioksida ini mempunyai kepentingan yang signifikan kepada kesihatantubuh manusia Dalam kajian ini sebanyak 42 aksesi padi bukit bewarna diperolehi dariInstitut Penyelidikan Padi Antarabangsa (IRRI) Ia terdiri daripada koleksi pelbagaitempat dari seluruh dunia Untuk mendedahkan kepelbagaian genetic antara aksesi 25penanda SSR telah digunakan dalam kajian ini Daripada 25 penanda SSR digunakandalam kajian ini hanya 21 yang polimorfik Min He adalah 0470 dan indeks informasiShannons adalah antara julat daripada 0380 sehingga 1660 Daripada penanda SSRanalisis kluster menggunakan ldquoJaccardSimiliarity Coefficientrdquo menunjukkan kesemuaaksesi telah diklusterkan sebanyak 7 kumpulan Biji benih antara aksesi telah ditanamdi rumah kaca untuk multiplikasi ciri-ciri penilaian morfologi dan agronomimenggunakan model RCBD dengan 3 replikasi bagi setiap aksesi Parameter tersebuttelah dikumpulkanbilanganbatang per pokok bilangan tangkai per pokok tinggipokok panjang daun bendera panjang tangkai buah terisi per tangkai buah tak terisiper tangkai indeks tuaian hasil per pokok 100 berat buah hari untuk berbunga hari
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untuk matang nisbah panjang lebar biji panjang biji kandungan klorofil (bacaan spad)pada 40 dan 60 hari Kesemua data ini telah dianalisi smenggunakan perisian SAS 92Ciri-cirimorfologi dan agronomi menunjukkan signifikasi pada variasi antara semuaaksesi Keterwarisan daripada 25 ciri-ciri agro-morfologi dan kandungan nutrisi(makroampmikro) dalam jerami pad antara julat dari 5652 sehingga 9931 Kandungannutrisi (makroampmikro) dalam biji padi amat berbeza antara aksesi Aktiviti antioksidauntuk kesemua aksesi padi ditentukan oleh kaedah radika memerangkap 11- Diphenyl-2-picrylhydazyl (DPPH) antara jula tdari 3185 sehingga 9845 Berdasarkankandungan vitamin E (tocochromanols) kandungan ldquotocotrienolrdquo adalah tinggi daripadaldquotocopherolrdquo bagi semua aksesi Pemilihan untuk aksesi beras yang lebih baik untukprogram pembiakbakaan boleh dibuat menggunakan maklumat daripada agro-morfologidan status nutrisi aksesi
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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1
CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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untuk matang nisbah panjang lebar biji panjang biji kandungan klorofil (bacaan spad)pada 40 dan 60 hari Kesemua data ini telah dianalisi smenggunakan perisian SAS 92Ciri-cirimorfologi dan agronomi menunjukkan signifikasi pada variasi antara semuaaksesi Keterwarisan daripada 25 ciri-ciri agro-morfologi dan kandungan nutrisi(makroampmikro) dalam jerami pad antara julat dari 5652 sehingga 9931 Kandungannutrisi (makroampmikro) dalam biji padi amat berbeza antara aksesi Aktiviti antioksidauntuk kesemua aksesi padi ditentukan oleh kaedah radika memerangkap 11- Diphenyl-2-picrylhydazyl (DPPH) antara jula tdari 3185 sehingga 9845 Berdasarkankandungan vitamin E (tocochromanols) kandungan ldquotocotrienolrdquo adalah tinggi daripadaldquotocopherolrdquo bagi semua aksesi Pemilihan untuk aksesi beras yang lebih baik untukprogram pembiakbakaan boleh dibuat menggunakan maklumat daripada agro-morfologidan status nutrisi aksesi
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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ACKNOWLEDGEMENT
In the name of Allah the Most Gracious the Most merciful I would like to praise to theAllah Almighty for His blessings which enable me to complete my thesis I would liketo express my appreciation to my supervisor Professor Dr Mohamed Hanafi Musa forhis guidance good advice and idea from beginning to the end of this research Withouthis supports and encouragement my research study may not finished on the time
I would like to give special thanks to the members of the Advisory CommitteeProfessor Dr MohdRafiiYusop and Professor Datin Dr SitiNorAkmar Abdullah fortheir good advice and suggestion for my research study
I am thankful to Universiti Putra Malaysia for awarding me scholarship and researchfacilities for my master study Additionally I want to acknowledge for the Long-termResearch Grant Scheme (LRGS 55525001Food Security) for the financial support toconduct this research
I wish to give thanks to all the staff of Institute of Tropical Agriculture (ITA) UPMespecially to Mrs Norhasimah Mr Zainuddin Mr Zahardin and Mrs NorRafidah fortheir help during my research and study period Furthermore I would like to thankAssociate Professor Dr SharifahKharidha Syed Muhamad and DrAzmilHaizam
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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REFERENCES
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Allard RW (1960) Principles of Plant Breeding John Whiley Sons Inc NewYork pp 485
Ali SS Jafri SJH Khan TZ Mahmood A Butt MA (2000)Heritability ofyield and yield components of rice Pakistan Journal of AgriculturalResearch 16 89-91
Angela H GraziellaB Claude D Francisco M Martin C (2009) Plant rootgrowth architecture and function Plant Soil 321 153-187
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Barker R(1986) Setting priorities for rice research in West Africa Paper presentedat the seminar of the International Rice Research Institute Los BanosAugust 1986
Bergman CJ and Xu Z (2003) Genotype and environment effects on the tocolsand gamma-oryzanol contents of Southern US rice Cereal Chemistry 80446-449
Bhutta WM (2006) Role of some agronomic traits for grain yield production inwheat (Triticum aestivum L) genotypes under drought conditions RevistaUDO Agricola 6 11-19
Bisne R Sarawgi AK Verulkar B (2009) Study of heritability GeneticAdvance and Variability for Yield Contributing Characters in RiceBangladesh Journal of Agriculture 34175-179
Brush SB (1995) In situ conservation of landraces in centers of crop diversityCrop Science 35 346-354
Bryan FJ Manly (2004) Multivariate Statistical Methods A Primer third editionUSA Chapman and HallCRC pp 75
Bucio JL Ramirez AC Estrella LH (2003) The role of nutrient availability inregulating root architecture Current Opinion in Plant Biology 6280-287
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Burton GW (1952) Quantitative inheritance in grasses Proceedings of the 6thgrassland Congress 1277-285
Butsat S and Siriamornpun S (2010) Antioxidant capacities and phenoliccompounds of the husk bran and endosperm of Thai rice Food Chemistry119 606-613
Causse MA Fulton TM Cho YG Ahn SN Chunwongse J Wu K XiaoJ Yu Z Ronald PC Harrington SE Second G McCouch SRTanksley SD (1994) Saturated molecular map of the rice genome based onan interspecific backross population Genetics 138 1251-1274
Chakravarthi BK and Naravaneni R (2006) SSR marker based DNAfingerprinting and diversity study in rice (Oryza sativa L) African Journalof Biotechnology 5 684-688
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Ahmad Tarmizi for giving permission to use the lab facilities in UPM-Bernas andMalaysia Palm Oil Board (MPOB) laboratories respectively
I am thankful to my friends in ITA laboratory especially to Dr Jannatul Dr NusaibahMs Mayzaitul Ms Akmal Mrs Shuhada Mr Hanif Ms Yee Min Mr ShahrudinMr Mahboud Mrs Hasmah and to all individual who helped me directly or indirectlyduring the tenure of my research
Special appreciation goes to my beloved parents Mr Ahmad Bin MohamadSom andMrs SoarsquoatBintiJohari for their blessings and encouragements to me to finish thestudies Special gratitude also to my siblings who also gave me moral support duringmy study
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted asfulfillment of the requirement for the degree of Master of Science The members of theSupervisory Committee were as follows
Mohamed Hanafi Bin Musa PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Chairman)
Mohd Rafii Bin Yusop PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
Datin Siti Nor Akmar Binti Abdullah PhDProfessorInstitute of Tropical AgricultureUniversiti Putra Malaysia(Member)
BUJANG BIN KIM HUATPhDProfessor and DeanSchool of Graduate StudiesUniversiti Putra Malaysia
Date
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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DECLARATION
Declaration by graduate student
I hereby confirm thatbull this thesis is my original workbull quotations illustrations and citations have been duly referencedbull this thesis has not been submitted previously or concurrently for any other
degree at any other institutionsbull intellectual property from the thesis and copyright of thesis are fully-owned
by Universiti Putra Malaysia as according to the Universiti Putra Malaysia(Research) Rules 2012
bull written permission must be obtained from supervisor and the office ofDeputy Vice-Chancellor (Research and Innovation) before thesis is published(in the form of written printed or in electronic form) including booksjournals modules proceedings popular writings seminar papersmanuscripts posters reports lecture notes learning modules or any othermaterials as stated in the Universiti Putra Malaysia (Research) Rules 2012
bull there is no plagiarism or data falsificationfabrication in the thesis andscholarly integrity is upheld as according to the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti PutraMalaysia (Research) Rules 2012 The thesis has undergone plagiarismdetection software
Signature _________________ Date __________________
Name and Matric No FAIZ AHMAD (GS28493)
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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Declaration by Members of Supervisory Committee
This is to confirm thatbull the research conducted and the writing of this thesis was under our supervisionbull supervision responsibilities as stated in the Universiti Putra Malaysia
(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to
Signature ________________ Signature ______________________Name of Name ofChairman of Member ofSupervisory SupervisoryCommittee ________________ Committee _____________________
Signature ___________________Name ofMember ofSupervisoryCommittee ___________________
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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2
There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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TABLE OF CONTENTSPage
ABSTRACT iABSTRAK iiiACKNOWLEDGEMENT vAPPROVAL viiDECLARATION ixLIST OF TABLES xivLIST OF FIGURES xvLIST OF ABBREVIATIONS xviiCHAPTER1 INTRODUCTION 12 LITERATURE REVIEW 321 Origin and Distribution of Rice 322 Botany and Taxonomic classification of Oryza sativa L 323 Coloured upland rice germplasm 424 Medicinal value of coloured upland rice germplasms 525 Growth and development of the rice plant 5251 Vegetative stage 6252 Reproductive stage 6253 Ripening stage 626 Genetic diversity 627 Heritability and genetic advanced 728 Simple sequence repeated marker 729 Mineral and antioxidant activities of the rice 8210 Tocochromanols 82101 Tocopherol 92102 Tocotrienol 93 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSIONS BY SSR MARKERS11
31 Introduction 1132 Objectives 1233 Materials and methods 12331 Plant materials 12332 DNA extraction 12333 PCR amplification 12
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
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334 Gel documentation 13335 Data analysis 1334 Results and discussion 16341 Characterization of SSR markers 16342 Clustering analysis 20343 Principle component analysis 2435 Conclusions 264 ASSESSMENT OF GENETIC DIVERSITY OF RICE
ACCESSSIONS BY QUANTITATIVE TRAITS27
41 Introduction 2742 Objectives 2743 Materials and methods 28431 Plant materials 28432 Experimental location 28433 Preparation of the soil medium and fertilizer 28434 Raising of rice seedling 28435 Management of the rice plant 28436 Agro-morphological characteristics 28437 Nutrient content in rice straw 29438 Statistical analysis 30439 Genetic variation of rice plant 3044 Results and discussion 31441 Agro-morphological data 31442 Nutrient content of rice accessions in rice straw 52
443 Correlation among agro-morphological data and rice strawnutrient content
58
444 Genetic variation parameters in rice plant 60445 Clustering analysis 62446 Principal component analysis 6445 Conclusions 675 NUTRIENT CONTENT ANTIOXIDANT ACTIVITY
AND TOCOCHROMANOLS CONTENT OFCOLOURED RICE ACCESSIONS
69
51 Introduction 6952 Objectives 6953 Materials and methods 69531 Plant materials 69532 Sample preparation 70
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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533 Determination of nutrient contents 70534 Determination of antioxidant activities 70535 Determination of tocochromanols content 70536 Statistical analysis 7154 Results and discussion 71541 Nutrient content of rice accession seed 71542 Antioxidant activities of rice accessions 78543 Tocochromanols content of selected rice accessions 8155 Conclusions 856 GENERAL CONCLUSION AND RECOMMENDATION 8661 General conclusion 8662 Recommendations for future research 87REFERENCES 88APPENDICES 101BIODATA OF STUDENT 111LIST OF PUBLICATIONS 112
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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LIST OF TABLES
Table Page21 The tocopherol and tocotrienol content in some cereal types 931 List of selected coloured upland rice accessions 1432 List of information SSR primers used in this study 1533 Allelic variation among polymorphic SSR loci 1634 Genetic diversity parameters information 1835 Data on chromosome number expected allele range observed
allele range and difference between amplified allele20
36 Grouping of the rice accessions based on the dendrogramfrom SSR marker
23
37 Grouping of the accessions based on the principle componentanalysis from SSR marker
26
41 ANOVA table and variance component of estimation 3042 Mean squares of analysis of variance for 16 agro-
morphological characteristic among 42 rice accessions32
43 Classification of rice kernel length and shape 4444 Mean squares of analysis of variance for nutrient content in
rice straw among 42 rice accessions53
45 Pearsonrsquos correlation coefficient among 16 agro-morphologicaltraits and nutrient (rice straw) of 42 rice accessions
58
46 Estimation of genetic variables for 16 agro-morphologicaltraits and nutrients content (rice straw) among 42 riceaccessions
62
47 Grouping of the rice accessions based on the dendrogramfrom 16 agro-morphological characteristics
64
48 Eigen vectors and eigen values of the first five principalcomponents from 16 agro-morphological characteristics
67
51 Mean square of analysis of variance for nutrient content in riceseed among 42 coloured upland rice accessions
72
52 Mean square of analysis of variance for DPPH free radicalscavenging effect among 42 coloured upland rice accessions
79
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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LIST OF FIGURESFigure Page21 Red and purple coloured rice seeds 422 Growing stage of the rice plant 523 The structures of tocopherol and tocotrienols 1031 The monomorphic and polymorphic bands for marker RM 431
and RM 413 among 21 accessions17
32 Dendrogram constructed from SSR marker analysis 2233 The pedigree structures of the 3 breeding lines 2434 Three dimensional view of principle component
using 25 SSR markers25
41 Number of tillers among 42 coloured upland rice accessions 3342 Number of panicles among 42 coloured upland rice accessions 3443 Plant height among among 42 coloured upland rice accessions 3644 Length of flag leaf among 42 coloured upland rice accessions 3745 Panicle length among 42 coloured upland rice accessions 3846 Percentage of filled grain among 42coloured
upland rice accessions40
47 Harvest index among 42 coloured upland rice accessions 4148 Grain yield per plant among 42 coloured upland rice accessions 4249 Hundred grain weight among 42 coloured upland rice accessions 43410 Kernel length among 42 coloured upland rice accessions 45411 Kernel shape among 42 coloured upland rice accessions 46412 Days to flowering among 42 coloured upland rice accessions 48413 Days to maturity among 42 coloured upland rice accessions 49414 Chlorophyll SPAD value at 40 days and 60 days after
planting among 42 coloured upland rice accessions51
415 Nitrogen content in rice straw among 42 colouredupland rice accessions
55
416 Macro-nutrient content among 42 coloured upland riceaccessions
56
417 Micro-nutrient contentamong 42 coloured upland riceaccessions
57
418 Dendrogram constructed based on 16 agro-morphologicalcharacteristics
63
419 Three dimensional view of principle component analysisusing 16 morphological and agronomical characteristics
66
51 Nitrogen content in rice seed among 42 coloured uplandrice accessions
75
52 Macro-nutrient content among 42 coloured upland riceaccessions
76
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53 Micro-nutrient content among 42 coloured upland riceaccessions
77
54 Free radical scavenging effect among 42 coloured upland riceaccessions
80
55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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53 Micro-nutrient content among 42 coloured upland riceaccessions
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54 Free radical scavenging effect among 42 coloured upland riceaccessions
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55 The correlation between tocopherol and tocotrienolscontent among 6 selected coloured upland rice accessions
82
56 Tocopherol and tocotrienol content among 6 selectedcoloured upland rice accessions
83
57 Isomer of tocopherol and tocotrienol content among6 selected coloured upland rice accessions
84
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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LIST OF ABBREVIATIONS
- Percentageα - Alpha β - Beta γ - Gama δ - Delta σ2g - Genotypic variance σ2p - Phenotypic variance degC - Degree celsiusANOVA - Analysis of varianceB - Boronbp - Base pairCa - Calciumcm - CentimeterCTAB - Cetyltrimethyl ammonium bromideCu - CopperDNA - Deoxyribose nucleic aciddNTPs - Deoxyribonucleotide triphosphateEDTA - Ethylene diaminetetracetateFe - IronGA - Genetic advanceg - GramGCV - Genotypic coefficient varianceH2SO4 Sulphuric acidH202 - Hydrogen peroxideh2B - HeritabilityHe - Expected heterozygosityIRRI - International Rice Research InstituteK - PotassiumL - LiterM - MolarMg - Magnesiummg - Milligrammm - MilimetermM - Millimolarmin - MinutemL - MilliliterMn - ManganeseMo - MolybdenumN - NitrogenNaCl - Sodium Chloride
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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P - PhosphorusPCR - Polymerase chain reactionPIC - Polymorphic information contentPVP - Polyvinylpolypyrrolidonerpm - Rotation per minuteSSR - Short sequence repeatedTBE - Tris-borate-EDTAUV - Ultravioletmicrog - MicrogrammicroL - MicroliterV - Voltvv - Volume per volumewv - Weight per volumeZn - Zinc
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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HT UPM
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CHAPTER 1
INTRODUCTION
Rice is the staple food for most Asian countries including Malaysia Thailand andPhilippines Currently the level of rice sufficiency in Malaysia is at 72 and theyield at about 38 thaseason (Oryza 2012) The government had spent millionsof ringgit to increase domestic rice production and to cut the rice import This isdue to the food crisis in 2008 where countries such as Thailand Vietnam andPhilippines have reduced their rice export This problem caused the shortage ofrice during that period In 2011 the Malaysian Government had spent about RM266 million under the Economic Transformation Plan (ETP) to introduce thefragrant rice in non granary area (ETP 2011) About RM 300 million were spentby the government in order to increase the domestic rice production within theperiod of 8 to 9 years (Oryza 2012) This investment is very important action toreduce the importation of rice to increase the farmers income and as a foodsecurity programme
The world population is increasing and has reached 7 billion in 2011 Thepopulation will reach around 8 billion by 2025 (Rosenberg 2012) About half ofthe populations depend on rice as a main food source especially people from theAsian countries The reduction in productive rice area is the major problemfacing us today Inconvenient divergence will occur if the sufficiency to feedpeople is less than the demand Many alternative ways have been done toincrease rice production such as developing high yielding varieties resistant todiseases and pests introducing sustainable management practice to farmers andintroducing non granary area for planting rice
Upland rice can grow in non-flooded soil without the need for irrigation systemIt has special characteristics such as fragrance colour and shape (Hanafi et al2009) Usually upland rice is planted on the hills and the yield is very lowcompared to irrigated rice In Malaysia the cultivation of upland rice has beenperformed mainly by farmers in upland area in Peninsular Sabah and SarawakThe worldwide rice production and planted area is about 4 and 13 respectively(Gupta and Orsquotoole 1986) The main problem of the upland rice cultivation is tolow number of tillers lodging and imbalanced supply of nutrients Moreresearch is required to increase the yield of upland rice as an alternative toirrigated rice since the scarcity of granary areas
Health-conscious people is increasing in this modern society They prefer tochoose healthy and nutritious food in their daily meal The composition of themineral elements in food is decreasing during 1979-1995 period (Ya-Wen et al2004) The increasing case of chronic disease nowadays are also related tonutrient deficiency in food Thus coloured upland rice is one of the alternativesfor healthy food since it contains high antioxidant that has significant effect onhuman health This pigmented rice accession have potential use for breedingprogramme that is beneficial for various neutraceutical and functional fooddevelopment Thus assessments of the nutrient in these acccessions is importantfor better understanding and knowledge of coloured rice germplasms
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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FardetA Rock E Remesy C (2008) Is the in vitro antioxidant potential ofwhole-grain cereals and cereal products well reflected in vivo Journal ofCereal Science 48 (2008) 258-276
Fasahat P Muhammad K Abdullah A Ratnam W (2012) Proximatenutritional composition and antioxidant properties of Oryza rufipogon a
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wild rice collected from Malaysia compared to cultivated rice MR 219Australian Journal of Crop Science 6 1502-1507
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Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
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There are little information and research about the coloured upland riceaccessions The documentation of the accession must be done in order for furtherbreeding programme Agro-morphological data are the important characteristicneeded to select the good quality accessions Each accession has a uniquevarietal characteristic such as plant height panicle length and time of floweringWhile molecular markers is another tool used for selection of the accession forbreeding programe These include Restriction Fragment Length Polymorphism(RFLP) Amplified Fragment Length Polymorphism (AFLP) Simple SequenceRepeats (SSR) and Single Nucleotide Polymorphism (SNP) The most widelyused is SSR since it has high polymorphism and high reproducibility Molecularmarker is more powerful compared to morphology characteristic since it is notinfluenced by the environment
Documentation of the accessions must be done for better understanding andreveal the special characteristic of the accessions Hence the nutritional value ofthe acccession must be assessed to improve the the quality of upland rice Thisstudy was conducted to determine the genetic diversity and nutritional qualities of42 coloured upland rice germplasm of rice (Oryza sativa L) obtained from theInternational Rice Research Institute Philippines The specific objectives were
i) To assess genetic diversity using SSR markers and calculate genetic similaritiesamong accessionsii) To determine agro-morphological characteristics heritability and geneticadvanceiii) To determine the mineral content antioxidant activities and Vitamin Econtent
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HT UPM
90
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Claudia AP Torres LB Jose CR Alfredo IL Enrique D Sunethra E MarkLuis HE (2008) Phosphate availability alters lateral root development inArabidopsis by modulating auxin sensitivity via mechanism involving theTIR1 auxin receptor Plant Cell 203258-3272
Clifford MN (2000) Anthocyanins Nature occurence and dietary burden Journalof Agricultural and Food Chemistry 80 1063-1072
Colombo ML (2010) An update on vitamin E tocopherol and tocotrienolperspectives Molecules 15 2103-2113
Deka SC and Sood DR (2003) Studies on cooking behaviour of basmati ricegenotypes during storage Journal of Dairying Foods and Home Science 221-9
DellaPenna D (2005) Progress in the dissection and manipulation of vitamin Esynthesis Trends in Plant Science 12574-579
Duminil J Di Michele M (2009) Plant Species delimination A Comparison ofMorphological Moleculars Markers Plant Biosystems pp 1-15
Duwayri M Tran DV Nguyen VN (2000) Reflections on yield gaps in riceproduction how to narrow the gaps binding the rice yield gap in the Asia-Pacific region httpwwwfaoorg Accessed on 20 January 2013
Epstein SS Forsyth J Saporoschetz IB Mantel N (1966) An exploratoryinvestigation on the inhibition of elected photosensitizers by agents ofvarying antioxidant activity Radiation Research 28 322-335
ETP (2011) Introducing fragrant rice variety for non-irrigated areashttpwwwetppemandugovmy Accessed on 20 February 2013
Evans HM and Bishop KS (1922) Fetal resorption Science 55 650
Fairhurst TH and Dobermann A (2002) Rice in the global food supply BetterCrop International 163-6
Falk J and Bosch SM (2010) Tocochromanol function in plants antioxidationand beyond Journal of Experimental Botany 61 15491566
FardetA Rock E Remesy C (2008) Is the in vitro antioxidant potential ofwhole-grain cereals and cereal products well reflected in vivo Journal ofCereal Science 48 (2008) 258-276
Fasahat P Muhammad K Abdullah A Ratnam W (2012) Proximatenutritional composition and antioxidant properties of Oryza rufipogon a
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HT UPM
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wild rice collected from Malaysia compared to cultivated rice MR 219Australian Journal of Crop Science 6 1502-1507
FinocchiaroF Ferrari B GianinettiA AstaCD Galaverna G ScazzinaFPellegrini N (2007) Characterization of antioxidant compounds of red andwhite rice and changes in total antioxidant capacity during processingMolecular Nutrition and Food Research 51(2007) 1006 ndash 1019
Forde B and Lorenzo H (2001) The nutritional control of root developmentPlant Soil 23251-68
Frei M and Becker K (2003) Studies on the in vitro starch digestibility and theglycemic index of six different indigenous rice cultivars from thePhilippines Food Chemistry 83 395-402
Fuentes JL Cornide MT Alvarez ASuarez E Borges E (2005) Geneticdiversity analysis of rice varieties (Oryza sativa L) based on morphologicalpedigree and DNA polymorphism data Plant Genetics Resources 3 353-359
Gahoonia TS amp Nielsen NE (2004) Root traits as tools for creating phosphorusefficient varieties Plant and Soil 260 47-57
El-Gammal MI and Shakour AA (2001) Emission of pollutant from harvest andburning of rice straw in Egypt villages (North East of Nile Delta) Journal ofUnion of Arab Biologist 15 191-206
Garris AJ Tai TH Coburn J Kresovich S McCouch S (2005) Geneticstructure and diversity in Oryza sativa L Genetics 169 1631-1638
Ge Zhang B Xian Chen Q Bo Luo S Yuan Zhang C Yang Q Dong Liu K(2012) Effect of NPK Defeciencies on Root Architetecture and Growth ofCucumber International Journal of Agriculture and Biology 14 145-148
Goffman FD and Bergman CJ (2004) Rice kernel phenolic content and itsrelationship with antiradical efficiency Journal of the Science of Food andAgriculture 84 1235-1240
Gramene (2006)Oryza taxonomy httpwwwgrameneorg Accessed on 20January 2013
Grams GW Blesin CW Inglett GE (1970) Distribution of tocopherols withinthe corn kernel Journal of the American Oil Chemistsrsquo Society 47337-339
Gupta PC and Orsquotoole JC (1986) Upland rice A global perspectiveInternational Rice Research Institute Los Banos Laguna Philippines POBox 933 Manila Philipines
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Hanafi MM Hartinie A Shukor J Mahmud TMM (2009) Upland ricevarieties in Malaysia agronomic and soil physico-chemical characteristicsPertanika Journal of Tropical Agricultural Science 32 225-246
HargroveT and Coffman WR (2006) Breeding history Rice Today 5 35-38
Hartinee A (2006) Increasing the yield of upland rice in idle land through nutrientand weed management Unpublished master dissertation University PutraMalaysia Malaysia
Harushima Y Yano M Shomura A Sato M Shimano T Kuboki YYamamoto T Lin SY Antonio BA Parco A Kajiya H Huang NYamamotoK Nagamura Y Kurata N Khush GS Sasaki T (1998) Ahigh density rice genetic linkage map with 2275 markers using a single F2population Genetics 148479-494
Holasova M (1997) Distribution of tocopherols and tocotrienols in the mainproducts of wheat and rye milling Czech Journal of Food Science 15 343-350
Holasova M Velisek J Davidek J (1995) Tocopherol and tocotrienol contentsin cereal grains Czech Journal of Food Science13 409-417
Hotz C and Brown KH (2004) Assessment of the risk of zinc dificiency inpopulations Food and Nutrition Bulletin 25 130-162
Hu C Zawistowski J Ling W Kitts DD (2003) Black rice (Oryza sativa Lindica) pigmented fraction suppresses both reactive oxygen species and nitricoxide in chemical and biological model systems Journal of Agricultural andFood Chemistry 51 5271-5277
Hu X Wang J Lu P Zhang H (2009) Assessment of Genetic Diversity inBroomcorn Millet (Panicum miliaceum L) using SSR markers Journal ofGenetics and Genomics 36 491-500
IRRI (2012) Sharing rice httpwwwirriorg Accessed on 18 December 2012
Islam MS Bhutya MSU Rahman S Hussain MM (2009) Evaluation ofSPAD and LCC Based Nitrogen Management in Rice (Oryza sativa L)Bangladesh Journal of Agriculture Research 34 661-672
Itani T And Ogawa M (2004) History and recent trends of red rice in JapanJapanese Journal of Crop Science 73 137-147
JhangT KaurM KaliaP and Sharma TR(2010) Efficiency of Different MarkerSystem for Molecular Characterization of Subtropical Carrot GermplasmJournal of Agriculture Science 148171-181
Jose LB Alfredo CR Luis HE (2003) The role of nutrient availability inregulating root architecture Current Opinion in Plant Biology 6280-287
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Johnson HW Robinson HP and Comstoc RE (1995) Estimation of Geneticand Environmental Variability in Soybeans Agronomy Journal 47314-318
Kang HW Cho YG Yoon UH Eun MY (1998) A Rapid DNA Extractionmethod for RFLP and PCR Analysis from a Single Dry Seed PlantMolecular Biology Reporter 161-9
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Lapitan VC Brar DS AbeT Redona ED (2007) Assessement of GeneticDiversity of Philippine Rice Cultivar Carrying Good Quality Traits usingSSR Markers Breeding Science 57263-270
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Lehmann J Martin HL Lashley EL Marshall MW Judd JT (1986)Vitamin E in foods from high and low linoleic acid diets Journal ofAmerican Dietetic Association 86 1208-1216
Lehmann JW Putnam DH Qureshi AA (1994) Vitamin E isomers in grainamaranths (Amaranthus spp) Lipids 29 177-181
Leon J and Schwang KU (1992) Description and application of a screeningmethod to determine root morphology traits of cereals cultivars Journal ofAgronomy and Crop Science 169 128-134
Linares OF (2002) African rice (Oryza glaberrima) history and future potentialIn Proceedings of The National Academy of Science of the United States ofAmerica 9916360-16365
Ling WH Cheng QX MaJ Wang T (2001) Red and black rice decreaseatherosclerotic plaque formation and increase antioxidant status in rabbitsJournal of Nutrition 131 1421-1426
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Lu BR Naredo MEB Juliano AB Jackson MT (2000) Preliminary studieson taxonomy and biosystematics of the AA genome Oryza species
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HT UPM
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Chun L Mi J G Li F Chen F Zhang F (2005) Genetic analysis of maize rootcharacteristics in response to low nitrogen stress Plant and Soil 369-382
Claudia AP Torres LB Jose CR Alfredo IL Enrique D Sunethra E MarkLuis HE (2008) Phosphate availability alters lateral root development inArabidopsis by modulating auxin sensitivity via mechanism involving theTIR1 auxin receptor Plant Cell 203258-3272
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Fairhurst TH and Dobermann A (2002) Rice in the global food supply BetterCrop International 163-6
Falk J and Bosch SM (2010) Tocochromanol function in plants antioxidationand beyond Journal of Experimental Botany 61 15491566
FardetA Rock E Remesy C (2008) Is the in vitro antioxidant potential ofwhole-grain cereals and cereal products well reflected in vivo Journal ofCereal Science 48 (2008) 258-276
Fasahat P Muhammad K Abdullah A Ratnam W (2012) Proximatenutritional composition and antioxidant properties of Oryza rufipogon a
copy COPYRIG
HT UPM
91
wild rice collected from Malaysia compared to cultivated rice MR 219Australian Journal of Crop Science 6 1502-1507
FinocchiaroF Ferrari B GianinettiA AstaCD Galaverna G ScazzinaFPellegrini N (2007) Characterization of antioxidant compounds of red andwhite rice and changes in total antioxidant capacity during processingMolecular Nutrition and Food Research 51(2007) 1006 ndash 1019
Forde B and Lorenzo H (2001) The nutritional control of root developmentPlant Soil 23251-68
Frei M and Becker K (2003) Studies on the in vitro starch digestibility and theglycemic index of six different indigenous rice cultivars from thePhilippines Food Chemistry 83 395-402
Fuentes JL Cornide MT Alvarez ASuarez E Borges E (2005) Geneticdiversity analysis of rice varieties (Oryza sativa L) based on morphologicalpedigree and DNA polymorphism data Plant Genetics Resources 3 353-359
Gahoonia TS amp Nielsen NE (2004) Root traits as tools for creating phosphorusefficient varieties Plant and Soil 260 47-57
El-Gammal MI and Shakour AA (2001) Emission of pollutant from harvest andburning of rice straw in Egypt villages (North East of Nile Delta) Journal ofUnion of Arab Biologist 15 191-206
Garris AJ Tai TH Coburn J Kresovich S McCouch S (2005) Geneticstructure and diversity in Oryza sativa L Genetics 169 1631-1638
Ge Zhang B Xian Chen Q Bo Luo S Yuan Zhang C Yang Q Dong Liu K(2012) Effect of NPK Defeciencies on Root Architetecture and Growth ofCucumber International Journal of Agriculture and Biology 14 145-148
Goffman FD and Bergman CJ (2004) Rice kernel phenolic content and itsrelationship with antiradical efficiency Journal of the Science of Food andAgriculture 84 1235-1240
Gramene (2006)Oryza taxonomy httpwwwgrameneorg Accessed on 20January 2013
Grams GW Blesin CW Inglett GE (1970) Distribution of tocopherols withinthe corn kernel Journal of the American Oil Chemistsrsquo Society 47337-339
Gupta PC and Orsquotoole JC (1986) Upland rice A global perspectiveInternational Rice Research Institute Los Banos Laguna Philippines POBox 933 Manila Philipines
copy COPYRIG
HT UPM
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Hanafi MM Hartinie A Shukor J Mahmud TMM (2009) Upland ricevarieties in Malaysia agronomic and soil physico-chemical characteristicsPertanika Journal of Tropical Agricultural Science 32 225-246
HargroveT and Coffman WR (2006) Breeding history Rice Today 5 35-38
Hartinee A (2006) Increasing the yield of upland rice in idle land through nutrientand weed management Unpublished master dissertation University PutraMalaysia Malaysia
Harushima Y Yano M Shomura A Sato M Shimano T Kuboki YYamamoto T Lin SY Antonio BA Parco A Kajiya H Huang NYamamotoK Nagamura Y Kurata N Khush GS Sasaki T (1998) Ahigh density rice genetic linkage map with 2275 markers using a single F2population Genetics 148479-494
Holasova M (1997) Distribution of tocopherols and tocotrienols in the mainproducts of wheat and rye milling Czech Journal of Food Science 15 343-350
Holasova M Velisek J Davidek J (1995) Tocopherol and tocotrienol contentsin cereal grains Czech Journal of Food Science13 409-417
Hotz C and Brown KH (2004) Assessment of the risk of zinc dificiency inpopulations Food and Nutrition Bulletin 25 130-162
Hu C Zawistowski J Ling W Kitts DD (2003) Black rice (Oryza sativa Lindica) pigmented fraction suppresses both reactive oxygen species and nitricoxide in chemical and biological model systems Journal of Agricultural andFood Chemistry 51 5271-5277
Hu X Wang J Lu P Zhang H (2009) Assessment of Genetic Diversity inBroomcorn Millet (Panicum miliaceum L) using SSR markers Journal ofGenetics and Genomics 36 491-500
IRRI (2012) Sharing rice httpwwwirriorg Accessed on 18 December 2012
Islam MS Bhutya MSU Rahman S Hussain MM (2009) Evaluation ofSPAD and LCC Based Nitrogen Management in Rice (Oryza sativa L)Bangladesh Journal of Agriculture Research 34 661-672
Itani T And Ogawa M (2004) History and recent trends of red rice in JapanJapanese Journal of Crop Science 73 137-147
JhangT KaurM KaliaP and Sharma TR(2010) Efficiency of Different MarkerSystem for Molecular Characterization of Subtropical Carrot GermplasmJournal of Agriculture Science 148171-181
Jose LB Alfredo CR Luis HE (2003) The role of nutrient availability inregulating root architecture Current Opinion in Plant Biology 6280-287
copy COPYRIG
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Johnson HW Robinson HP and Comstoc RE (1995) Estimation of Geneticand Environmental Variability in Soybeans Agronomy Journal 47314-318
Kang HW Cho YG Yoon UH Eun MY (1998) A Rapid DNA Extractionmethod for RFLP and PCR Analysis from a Single Dry Seed PlantMolecular Biology Reporter 161-9
Lai J Dey N Kim CS (2004) Characterization of the maize endospermtranscriptome and its comparison to the rice genome Genome Research 141932-1937
Lapitan VC Brar DS AbeT Redona ED (2007) Assessement of GeneticDiversity of Philippine Rice Cultivar Carrying Good Quality Traits usingSSR Markers Breeding Science 57263-270
Lee SC Kim JH Jeong SM Kim DR Ha JU Nam KC Ahn DU(2003) Effect of far-infrared radiation on the antioxidant activity of ricehulls Journal of Agricultural and Food Chemistry 51 4400-4403
Lehmann J Martin HL Lashley EL Marshall MW Judd JT (1986)Vitamin E in foods from high and low linoleic acid diets Journal ofAmerican Dietetic Association 86 1208-1216
Lehmann JW Putnam DH Qureshi AA (1994) Vitamin E isomers in grainamaranths (Amaranthus spp) Lipids 29 177-181
Leon J and Schwang KU (1992) Description and application of a screeningmethod to determine root morphology traits of cereals cultivars Journal ofAgronomy and Crop Science 169 128-134
Linares OF (2002) African rice (Oryza glaberrima) history and future potentialIn Proceedings of The National Academy of Science of the United States ofAmerica 9916360-16365
Ling WH Cheng QX MaJ Wang T (2001) Red and black rice decreaseatherosclerotic plaque formation and increase antioxidant status in rabbitsJournal of Nutrition 131 1421-1426
Linkohr BI Williamson LC Fitter AH Leyser O (2002) Nitrate andphosphate availability and distribution have different effects on root systemarchitecture of Arabidopsis Plant Journal 29751-760
Londo JP Chiang YC Hung KH Chiang TY Schaal BA (2006)Phylogeography of Asian wild rice Oryza rufipogon reveals multipleindependent domestications of cultivated rice Oryza sativa Proceedings ofThe National Academy of Science USA 103 9578-9583
Lu BR Naredo MEB Juliano AB Jackson MT (2000) Preliminary studieson taxonomy and biosystematics of the AA genome Oryza species
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(Poaceae) In Jacobs SW Everett LJ eds Grasses Systematics andEvolution CSIRO Melbourne pp51-58
Lynch JP and Brown KM (2008) Root strategies for phosphorus acquisition InWhite PJ Hammond JP TheEcophysiology of Plant ndashPhosphorusInteractions Netherlands Springer pp 83-116
Ma Z Bielenberg DG Brown KM Lynch JP (2001) Regulation of root hairdensity by phosphorus availability in Arabidopsis thaliana Plant CellEnviron 24 459-467
Maekawa M and Kita T (1984) The spectral characteristic of extraction pigmentof the genetic colouring grain in rice plants Hotsukaido universityagricultural faculty Farm Research Report 23 11-21
Mantegazza R Biloni M Grassi F Basso B Lu BR (2008) Temporal trendsof variation in Italian rice germplasm over the past two centuries revealed byAFLP and SSR markers Crop Science 481832-1840
Mccall MR and Frei B (1999) Can antioxidant vitamins materially reduceoxidative damage in humans Free Radical Biology and Medicine 261034-1053
Meng F Wei Y Yang X (2005) Iron content and bioavailability in rice Journalof Trace Element in Medicine and Biology 18 333-338
Messmer MM Melchinger AE Boppenmayer J Brunklaus-Jung E HermanRG (1992) Relationship among Early European Maize (Zea mays L)inbreds I Genetic Diversity among Flint and Dent Lines Revealed byRFLPs Crop Science 321301-1309
Mia MAB and Shamsuddin ZH(2011) Physio-morphological appraisal ofaromatic fine rice (Oryza sativa L) in relation to yield potentialInternational Journal of Botany 7 223-229
Miyazawa T Shibata A Sookwong P Kawakami Y Eitsuka T Asai AOikawa S Nakagawa K (2009) Antiangiogenic and anticancer potentialof unsaturated vitamin E (tocotrienol) The Journal of NutritionalBiochemistry 20 79-86
Molina J SikoraM Garud N Flowers JM Rubinstein S Reynolds AHuang P Jackson S Schaal BA Bustamante CD Boyko ARPurugganan MD (2011) Molecular evidence for a single evolutionaryorigin of domesticated rice PNAS 108 8351-8356
Mondini L Noorani A Pagnotta A (2009) Assessing plant genetic diversity bymolecular tools Diversity 1 19-35
Morgante M And Olivieri AM (1993) PCR- amplified microsatelites as markersin plant genetics Plant Journal 3 175-182
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Morishima H (2001) Evolution and domestication of rice In Khush GS BrarDS Hardy B eds RiceGenetics IV Proceedings of the FourthInternational Rice Genetics Symposium International Rice Research IntituteLos Banos Pp 63-77
Muntana N And Prasong S (2010) Study on total phenolic contents and theirantioxidant activities of thai white red and blck rice bran extracts PakistanJournal of Biological Sciences 13 170-174
Nesaretnam K (2008) Multitarget therapy of cancer by tocotrienols Cancerletters 269388-395
Norzaleha K Muhammad K Hamid AA S Mohamed Total phenolic contentsand antioxidant capacities of different coloured Malaysian rice grains Paperpresented at University Malaysia Terengganu Annual SymposiumTerengganu July 2012
Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
Oki T Masuda M Kobayashi M Nishiba Y Furuta S Suda I Sato T(2002) Polymeric procyanidins as radical- scavenging components in red-hulled rice Journal of Agricultural and Food Chemistry 50 7524-7529
Ong ASH (1993) Natural sources of tocotrienols In Packer L and Fuchs SVitamin E in Health and Disease New York Dekker pp 3-8
Oryza (2012) Malaysia Launches Project to Double Rice Output in 9 Yearshttpwwworyzacommalaysia-launches-project-double-rice-output-9-Accessed on 18 April 2013
OrsquoToole JC and Bland WL (1987) Genotypic variation in crop plant rootsystems Advance in Agronomy 4191-143
Panse VG and Sukhatme PV (1957) Genetics and Quantitative Characters inRelation to Plant Breeding Indian Journal Genetics 17 312-328
Peterson DM and Wood DF (1997) Composition and structure of high oil oatJournal of Cereal Science 26 121-128
Piironen V Syvaoja E-L Varo P Salminen K Koivistoinen P (1986)Tocopherols and tocotrienols in cereal products from Finland CerealChemistry 63 78-81
Peacuterez-Jimeacutenez J Arranz S Tabernero M Diaz-Rubio ME Serrano J GoniI Saura-Calixto F (2008) Updated methodology to determine antioxidantcapacity in plant foods oils and beverages Extraction measurement andexpression of results Food Research International 41 274-285
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Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
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ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
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Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
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Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
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Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
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Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
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Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
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Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
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Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
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HT UPM
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Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
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Burton GW (1952) Quantitative inheritance in grasses Proceedings of the 6thgrassland Congress 1277-285
Butsat S and Siriamornpun S (2010) Antioxidant capacities and phenoliccompounds of the husk bran and endosperm of Thai rice Food Chemistry119 606-613
Causse MA Fulton TM Cho YG Ahn SN Chunwongse J Wu K XiaoJ Yu Z Ronald PC Harrington SE Second G McCouch SRTanksley SD (1994) Saturated molecular map of the rice genome based onan interspecific backross population Genetics 138 1251-1274
Chakravarthi BK and Naravaneni R (2006) SSR marker based DNAfingerprinting and diversity study in rice (Oryza sativa L) African Journalof Biotechnology 5 684-688
Chanda SV and Nagani KV (2010) Antioxidant capacity of Manilkara zapota Lextracts evaluated by four in vitro methods Nature and Science 8 260-266
Chang TT (2003) Origin domestication and diversification In Smith CWDilday RH eds Rice Origin History Technology and Production JohnWiley amp Sons Hoboken New Jersey pp 3-25
Chang TT and Bardenas EA (1965) The morphology and varietalcharacteristics of the rice plant Technical bulletin 4 IRRI Philippines 40pp
Chang TT and Vergara BS (1975) Varietal diversity and morpho-agronomiccharacteristics of upland rice In IRRI Major Research on Upland RiceResearch on Upland Rice (pp 72-90) Philippines International RiceResearch Institute
Chaudhary RC and Tran DV Speciality rices of the world a prologue In DuffyR (2001) Speciality rices of the world breeding production and marketingUSA Science publisher 101-102
Chaudhary N and Khurana P (2009) Vitamin E biosynthesis in rice MolecularCharacterization Expression Profiling and Comparative PhylogeneticAnalysis Plant Science 177 479- 491
Chen MH Bergman CJ (2005) A rapid procedure for analysing rice bramtocopherol tocotrienol and β- oryzanol contents Journal of FoodComposition and Analysis 18 319-331
Choudhury B Khan ML Dayanandan S (2013) Genetic structure and diversityof indigenous rice (Oryza sativa) varieties in the Eastern Himalayan regionof Northeast India SpringerPlus 2228
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90
Chun L Mi J G Li F Chen F Zhang F (2005) Genetic analysis of maize rootcharacteristics in response to low nitrogen stress Plant and Soil 369-382
Claudia AP Torres LB Jose CR Alfredo IL Enrique D Sunethra E MarkLuis HE (2008) Phosphate availability alters lateral root development inArabidopsis by modulating auxin sensitivity via mechanism involving theTIR1 auxin receptor Plant Cell 203258-3272
Clifford MN (2000) Anthocyanins Nature occurence and dietary burden Journalof Agricultural and Food Chemistry 80 1063-1072
Colombo ML (2010) An update on vitamin E tocopherol and tocotrienolperspectives Molecules 15 2103-2113
Deka SC and Sood DR (2003) Studies on cooking behaviour of basmati ricegenotypes during storage Journal of Dairying Foods and Home Science 221-9
DellaPenna D (2005) Progress in the dissection and manipulation of vitamin Esynthesis Trends in Plant Science 12574-579
Duminil J Di Michele M (2009) Plant Species delimination A Comparison ofMorphological Moleculars Markers Plant Biosystems pp 1-15
Duwayri M Tran DV Nguyen VN (2000) Reflections on yield gaps in riceproduction how to narrow the gaps binding the rice yield gap in the Asia-Pacific region httpwwwfaoorg Accessed on 20 January 2013
Epstein SS Forsyth J Saporoschetz IB Mantel N (1966) An exploratoryinvestigation on the inhibition of elected photosensitizers by agents ofvarying antioxidant activity Radiation Research 28 322-335
ETP (2011) Introducing fragrant rice variety for non-irrigated areashttpwwwetppemandugovmy Accessed on 20 February 2013
Evans HM and Bishop KS (1922) Fetal resorption Science 55 650
Fairhurst TH and Dobermann A (2002) Rice in the global food supply BetterCrop International 163-6
Falk J and Bosch SM (2010) Tocochromanol function in plants antioxidationand beyond Journal of Experimental Botany 61 15491566
FardetA Rock E Remesy C (2008) Is the in vitro antioxidant potential ofwhole-grain cereals and cereal products well reflected in vivo Journal ofCereal Science 48 (2008) 258-276
Fasahat P Muhammad K Abdullah A Ratnam W (2012) Proximatenutritional composition and antioxidant properties of Oryza rufipogon a
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wild rice collected from Malaysia compared to cultivated rice MR 219Australian Journal of Crop Science 6 1502-1507
FinocchiaroF Ferrari B GianinettiA AstaCD Galaverna G ScazzinaFPellegrini N (2007) Characterization of antioxidant compounds of red andwhite rice and changes in total antioxidant capacity during processingMolecular Nutrition and Food Research 51(2007) 1006 ndash 1019
Forde B and Lorenzo H (2001) The nutritional control of root developmentPlant Soil 23251-68
Frei M and Becker K (2003) Studies on the in vitro starch digestibility and theglycemic index of six different indigenous rice cultivars from thePhilippines Food Chemistry 83 395-402
Fuentes JL Cornide MT Alvarez ASuarez E Borges E (2005) Geneticdiversity analysis of rice varieties (Oryza sativa L) based on morphologicalpedigree and DNA polymorphism data Plant Genetics Resources 3 353-359
Gahoonia TS amp Nielsen NE (2004) Root traits as tools for creating phosphorusefficient varieties Plant and Soil 260 47-57
El-Gammal MI and Shakour AA (2001) Emission of pollutant from harvest andburning of rice straw in Egypt villages (North East of Nile Delta) Journal ofUnion of Arab Biologist 15 191-206
Garris AJ Tai TH Coburn J Kresovich S McCouch S (2005) Geneticstructure and diversity in Oryza sativa L Genetics 169 1631-1638
Ge Zhang B Xian Chen Q Bo Luo S Yuan Zhang C Yang Q Dong Liu K(2012) Effect of NPK Defeciencies on Root Architetecture and Growth ofCucumber International Journal of Agriculture and Biology 14 145-148
Goffman FD and Bergman CJ (2004) Rice kernel phenolic content and itsrelationship with antiradical efficiency Journal of the Science of Food andAgriculture 84 1235-1240
Gramene (2006)Oryza taxonomy httpwwwgrameneorg Accessed on 20January 2013
Grams GW Blesin CW Inglett GE (1970) Distribution of tocopherols withinthe corn kernel Journal of the American Oil Chemistsrsquo Society 47337-339
Gupta PC and Orsquotoole JC (1986) Upland rice A global perspectiveInternational Rice Research Institute Los Banos Laguna Philippines POBox 933 Manila Philipines
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Hanafi MM Hartinie A Shukor J Mahmud TMM (2009) Upland ricevarieties in Malaysia agronomic and soil physico-chemical characteristicsPertanika Journal of Tropical Agricultural Science 32 225-246
HargroveT and Coffman WR (2006) Breeding history Rice Today 5 35-38
Hartinee A (2006) Increasing the yield of upland rice in idle land through nutrientand weed management Unpublished master dissertation University PutraMalaysia Malaysia
Harushima Y Yano M Shomura A Sato M Shimano T Kuboki YYamamoto T Lin SY Antonio BA Parco A Kajiya H Huang NYamamotoK Nagamura Y Kurata N Khush GS Sasaki T (1998) Ahigh density rice genetic linkage map with 2275 markers using a single F2population Genetics 148479-494
Holasova M (1997) Distribution of tocopherols and tocotrienols in the mainproducts of wheat and rye milling Czech Journal of Food Science 15 343-350
Holasova M Velisek J Davidek J (1995) Tocopherol and tocotrienol contentsin cereal grains Czech Journal of Food Science13 409-417
Hotz C and Brown KH (2004) Assessment of the risk of zinc dificiency inpopulations Food and Nutrition Bulletin 25 130-162
Hu C Zawistowski J Ling W Kitts DD (2003) Black rice (Oryza sativa Lindica) pigmented fraction suppresses both reactive oxygen species and nitricoxide in chemical and biological model systems Journal of Agricultural andFood Chemistry 51 5271-5277
Hu X Wang J Lu P Zhang H (2009) Assessment of Genetic Diversity inBroomcorn Millet (Panicum miliaceum L) using SSR markers Journal ofGenetics and Genomics 36 491-500
IRRI (2012) Sharing rice httpwwwirriorg Accessed on 18 December 2012
Islam MS Bhutya MSU Rahman S Hussain MM (2009) Evaluation ofSPAD and LCC Based Nitrogen Management in Rice (Oryza sativa L)Bangladesh Journal of Agriculture Research 34 661-672
Itani T And Ogawa M (2004) History and recent trends of red rice in JapanJapanese Journal of Crop Science 73 137-147
JhangT KaurM KaliaP and Sharma TR(2010) Efficiency of Different MarkerSystem for Molecular Characterization of Subtropical Carrot GermplasmJournal of Agriculture Science 148171-181
Jose LB Alfredo CR Luis HE (2003) The role of nutrient availability inregulating root architecture Current Opinion in Plant Biology 6280-287
copy COPYRIG
HT UPM
93
Johnson HW Robinson HP and Comstoc RE (1995) Estimation of Geneticand Environmental Variability in Soybeans Agronomy Journal 47314-318
Kang HW Cho YG Yoon UH Eun MY (1998) A Rapid DNA Extractionmethod for RFLP and PCR Analysis from a Single Dry Seed PlantMolecular Biology Reporter 161-9
Lai J Dey N Kim CS (2004) Characterization of the maize endospermtranscriptome and its comparison to the rice genome Genome Research 141932-1937
Lapitan VC Brar DS AbeT Redona ED (2007) Assessement of GeneticDiversity of Philippine Rice Cultivar Carrying Good Quality Traits usingSSR Markers Breeding Science 57263-270
Lee SC Kim JH Jeong SM Kim DR Ha JU Nam KC Ahn DU(2003) Effect of far-infrared radiation on the antioxidant activity of ricehulls Journal of Agricultural and Food Chemistry 51 4400-4403
Lehmann J Martin HL Lashley EL Marshall MW Judd JT (1986)Vitamin E in foods from high and low linoleic acid diets Journal ofAmerican Dietetic Association 86 1208-1216
Lehmann JW Putnam DH Qureshi AA (1994) Vitamin E isomers in grainamaranths (Amaranthus spp) Lipids 29 177-181
Leon J and Schwang KU (1992) Description and application of a screeningmethod to determine root morphology traits of cereals cultivars Journal ofAgronomy and Crop Science 169 128-134
Linares OF (2002) African rice (Oryza glaberrima) history and future potentialIn Proceedings of The National Academy of Science of the United States ofAmerica 9916360-16365
Ling WH Cheng QX MaJ Wang T (2001) Red and black rice decreaseatherosclerotic plaque formation and increase antioxidant status in rabbitsJournal of Nutrition 131 1421-1426
Linkohr BI Williamson LC Fitter AH Leyser O (2002) Nitrate andphosphate availability and distribution have different effects on root systemarchitecture of Arabidopsis Plant Journal 29751-760
Londo JP Chiang YC Hung KH Chiang TY Schaal BA (2006)Phylogeography of Asian wild rice Oryza rufipogon reveals multipleindependent domestications of cultivated rice Oryza sativa Proceedings ofThe National Academy of Science USA 103 9578-9583
Lu BR Naredo MEB Juliano AB Jackson MT (2000) Preliminary studieson taxonomy and biosystematics of the AA genome Oryza species
copy COPYRIG
HT UPM
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(Poaceae) In Jacobs SW Everett LJ eds Grasses Systematics andEvolution CSIRO Melbourne pp51-58
Lynch JP and Brown KM (2008) Root strategies for phosphorus acquisition InWhite PJ Hammond JP TheEcophysiology of Plant ndashPhosphorusInteractions Netherlands Springer pp 83-116
Ma Z Bielenberg DG Brown KM Lynch JP (2001) Regulation of root hairdensity by phosphorus availability in Arabidopsis thaliana Plant CellEnviron 24 459-467
Maekawa M and Kita T (1984) The spectral characteristic of extraction pigmentof the genetic colouring grain in rice plants Hotsukaido universityagricultural faculty Farm Research Report 23 11-21
Mantegazza R Biloni M Grassi F Basso B Lu BR (2008) Temporal trendsof variation in Italian rice germplasm over the past two centuries revealed byAFLP and SSR markers Crop Science 481832-1840
Mccall MR and Frei B (1999) Can antioxidant vitamins materially reduceoxidative damage in humans Free Radical Biology and Medicine 261034-1053
Meng F Wei Y Yang X (2005) Iron content and bioavailability in rice Journalof Trace Element in Medicine and Biology 18 333-338
Messmer MM Melchinger AE Boppenmayer J Brunklaus-Jung E HermanRG (1992) Relationship among Early European Maize (Zea mays L)inbreds I Genetic Diversity among Flint and Dent Lines Revealed byRFLPs Crop Science 321301-1309
Mia MAB and Shamsuddin ZH(2011) Physio-morphological appraisal ofaromatic fine rice (Oryza sativa L) in relation to yield potentialInternational Journal of Botany 7 223-229
Miyazawa T Shibata A Sookwong P Kawakami Y Eitsuka T Asai AOikawa S Nakagawa K (2009) Antiangiogenic and anticancer potentialof unsaturated vitamin E (tocotrienol) The Journal of NutritionalBiochemistry 20 79-86
Molina J SikoraM Garud N Flowers JM Rubinstein S Reynolds AHuang P Jackson S Schaal BA Bustamante CD Boyko ARPurugganan MD (2011) Molecular evidence for a single evolutionaryorigin of domesticated rice PNAS 108 8351-8356
Mondini L Noorani A Pagnotta A (2009) Assessing plant genetic diversity bymolecular tools Diversity 1 19-35
Morgante M And Olivieri AM (1993) PCR- amplified microsatelites as markersin plant genetics Plant Journal 3 175-182
copy COPYRIG
HT UPM
95
Morishima H (2001) Evolution and domestication of rice In Khush GS BrarDS Hardy B eds RiceGenetics IV Proceedings of the FourthInternational Rice Genetics Symposium International Rice Research IntituteLos Banos Pp 63-77
Muntana N And Prasong S (2010) Study on total phenolic contents and theirantioxidant activities of thai white red and blck rice bran extracts PakistanJournal of Biological Sciences 13 170-174
Nesaretnam K (2008) Multitarget therapy of cancer by tocotrienols Cancerletters 269388-395
Norzaleha K Muhammad K Hamid AA S Mohamed Total phenolic contentsand antioxidant capacities of different coloured Malaysian rice grains Paperpresented at University Malaysia Terengganu Annual SymposiumTerengganu July 2012
Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
Oki T Masuda M Kobayashi M Nishiba Y Furuta S Suda I Sato T(2002) Polymeric procyanidins as radical- scavenging components in red-hulled rice Journal of Agricultural and Food Chemistry 50 7524-7529
Ong ASH (1993) Natural sources of tocotrienols In Packer L and Fuchs SVitamin E in Health and Disease New York Dekker pp 3-8
Oryza (2012) Malaysia Launches Project to Double Rice Output in 9 Yearshttpwwworyzacommalaysia-launches-project-double-rice-output-9-Accessed on 18 April 2013
OrsquoToole JC and Bland WL (1987) Genotypic variation in crop plant rootsystems Advance in Agronomy 4191-143
Panse VG and Sukhatme PV (1957) Genetics and Quantitative Characters inRelation to Plant Breeding Indian Journal Genetics 17 312-328
Peterson DM and Wood DF (1997) Composition and structure of high oil oatJournal of Cereal Science 26 121-128
Piironen V Syvaoja E-L Varo P Salminen K Koivistoinen P (1986)Tocopherols and tocotrienols in cereal products from Finland CerealChemistry 63 78-81
Peacuterez-Jimeacutenez J Arranz S Tabernero M Diaz-Rubio ME Serrano J GoniI Saura-Calixto F (2008) Updated methodology to determine antioxidantcapacity in plant foods oils and beverages Extraction measurement andexpression of results Food Research International 41 274-285
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Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
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ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
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Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
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Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
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Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
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Chun L Mi J G Li F Chen F Zhang F (2005) Genetic analysis of maize rootcharacteristics in response to low nitrogen stress Plant and Soil 369-382
Claudia AP Torres LB Jose CR Alfredo IL Enrique D Sunethra E MarkLuis HE (2008) Phosphate availability alters lateral root development inArabidopsis by modulating auxin sensitivity via mechanism involving theTIR1 auxin receptor Plant Cell 203258-3272
Clifford MN (2000) Anthocyanins Nature occurence and dietary burden Journalof Agricultural and Food Chemistry 80 1063-1072
Colombo ML (2010) An update on vitamin E tocopherol and tocotrienolperspectives Molecules 15 2103-2113
Deka SC and Sood DR (2003) Studies on cooking behaviour of basmati ricegenotypes during storage Journal of Dairying Foods and Home Science 221-9
DellaPenna D (2005) Progress in the dissection and manipulation of vitamin Esynthesis Trends in Plant Science 12574-579
Duminil J Di Michele M (2009) Plant Species delimination A Comparison ofMorphological Moleculars Markers Plant Biosystems pp 1-15
Duwayri M Tran DV Nguyen VN (2000) Reflections on yield gaps in riceproduction how to narrow the gaps binding the rice yield gap in the Asia-Pacific region httpwwwfaoorg Accessed on 20 January 2013
Epstein SS Forsyth J Saporoschetz IB Mantel N (1966) An exploratoryinvestigation on the inhibition of elected photosensitizers by agents ofvarying antioxidant activity Radiation Research 28 322-335
ETP (2011) Introducing fragrant rice variety for non-irrigated areashttpwwwetppemandugovmy Accessed on 20 February 2013
Evans HM and Bishop KS (1922) Fetal resorption Science 55 650
Fairhurst TH and Dobermann A (2002) Rice in the global food supply BetterCrop International 163-6
Falk J and Bosch SM (2010) Tocochromanol function in plants antioxidationand beyond Journal of Experimental Botany 61 15491566
FardetA Rock E Remesy C (2008) Is the in vitro antioxidant potential ofwhole-grain cereals and cereal products well reflected in vivo Journal ofCereal Science 48 (2008) 258-276
Fasahat P Muhammad K Abdullah A Ratnam W (2012) Proximatenutritional composition and antioxidant properties of Oryza rufipogon a
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wild rice collected from Malaysia compared to cultivated rice MR 219Australian Journal of Crop Science 6 1502-1507
FinocchiaroF Ferrari B GianinettiA AstaCD Galaverna G ScazzinaFPellegrini N (2007) Characterization of antioxidant compounds of red andwhite rice and changes in total antioxidant capacity during processingMolecular Nutrition and Food Research 51(2007) 1006 ndash 1019
Forde B and Lorenzo H (2001) The nutritional control of root developmentPlant Soil 23251-68
Frei M and Becker K (2003) Studies on the in vitro starch digestibility and theglycemic index of six different indigenous rice cultivars from thePhilippines Food Chemistry 83 395-402
Fuentes JL Cornide MT Alvarez ASuarez E Borges E (2005) Geneticdiversity analysis of rice varieties (Oryza sativa L) based on morphologicalpedigree and DNA polymorphism data Plant Genetics Resources 3 353-359
Gahoonia TS amp Nielsen NE (2004) Root traits as tools for creating phosphorusefficient varieties Plant and Soil 260 47-57
El-Gammal MI and Shakour AA (2001) Emission of pollutant from harvest andburning of rice straw in Egypt villages (North East of Nile Delta) Journal ofUnion of Arab Biologist 15 191-206
Garris AJ Tai TH Coburn J Kresovich S McCouch S (2005) Geneticstructure and diversity in Oryza sativa L Genetics 169 1631-1638
Ge Zhang B Xian Chen Q Bo Luo S Yuan Zhang C Yang Q Dong Liu K(2012) Effect of NPK Defeciencies on Root Architetecture and Growth ofCucumber International Journal of Agriculture and Biology 14 145-148
Goffman FD and Bergman CJ (2004) Rice kernel phenolic content and itsrelationship with antiradical efficiency Journal of the Science of Food andAgriculture 84 1235-1240
Gramene (2006)Oryza taxonomy httpwwwgrameneorg Accessed on 20January 2013
Grams GW Blesin CW Inglett GE (1970) Distribution of tocopherols withinthe corn kernel Journal of the American Oil Chemistsrsquo Society 47337-339
Gupta PC and Orsquotoole JC (1986) Upland rice A global perspectiveInternational Rice Research Institute Los Banos Laguna Philippines POBox 933 Manila Philipines
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Hanafi MM Hartinie A Shukor J Mahmud TMM (2009) Upland ricevarieties in Malaysia agronomic and soil physico-chemical characteristicsPertanika Journal of Tropical Agricultural Science 32 225-246
HargroveT and Coffman WR (2006) Breeding history Rice Today 5 35-38
Hartinee A (2006) Increasing the yield of upland rice in idle land through nutrientand weed management Unpublished master dissertation University PutraMalaysia Malaysia
Harushima Y Yano M Shomura A Sato M Shimano T Kuboki YYamamoto T Lin SY Antonio BA Parco A Kajiya H Huang NYamamotoK Nagamura Y Kurata N Khush GS Sasaki T (1998) Ahigh density rice genetic linkage map with 2275 markers using a single F2population Genetics 148479-494
Holasova M (1997) Distribution of tocopherols and tocotrienols in the mainproducts of wheat and rye milling Czech Journal of Food Science 15 343-350
Holasova M Velisek J Davidek J (1995) Tocopherol and tocotrienol contentsin cereal grains Czech Journal of Food Science13 409-417
Hotz C and Brown KH (2004) Assessment of the risk of zinc dificiency inpopulations Food and Nutrition Bulletin 25 130-162
Hu C Zawistowski J Ling W Kitts DD (2003) Black rice (Oryza sativa Lindica) pigmented fraction suppresses both reactive oxygen species and nitricoxide in chemical and biological model systems Journal of Agricultural andFood Chemistry 51 5271-5277
Hu X Wang J Lu P Zhang H (2009) Assessment of Genetic Diversity inBroomcorn Millet (Panicum miliaceum L) using SSR markers Journal ofGenetics and Genomics 36 491-500
IRRI (2012) Sharing rice httpwwwirriorg Accessed on 18 December 2012
Islam MS Bhutya MSU Rahman S Hussain MM (2009) Evaluation ofSPAD and LCC Based Nitrogen Management in Rice (Oryza sativa L)Bangladesh Journal of Agriculture Research 34 661-672
Itani T And Ogawa M (2004) History and recent trends of red rice in JapanJapanese Journal of Crop Science 73 137-147
JhangT KaurM KaliaP and Sharma TR(2010) Efficiency of Different MarkerSystem for Molecular Characterization of Subtropical Carrot GermplasmJournal of Agriculture Science 148171-181
Jose LB Alfredo CR Luis HE (2003) The role of nutrient availability inregulating root architecture Current Opinion in Plant Biology 6280-287
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Johnson HW Robinson HP and Comstoc RE (1995) Estimation of Geneticand Environmental Variability in Soybeans Agronomy Journal 47314-318
Kang HW Cho YG Yoon UH Eun MY (1998) A Rapid DNA Extractionmethod for RFLP and PCR Analysis from a Single Dry Seed PlantMolecular Biology Reporter 161-9
Lai J Dey N Kim CS (2004) Characterization of the maize endospermtranscriptome and its comparison to the rice genome Genome Research 141932-1937
Lapitan VC Brar DS AbeT Redona ED (2007) Assessement of GeneticDiversity of Philippine Rice Cultivar Carrying Good Quality Traits usingSSR Markers Breeding Science 57263-270
Lee SC Kim JH Jeong SM Kim DR Ha JU Nam KC Ahn DU(2003) Effect of far-infrared radiation on the antioxidant activity of ricehulls Journal of Agricultural and Food Chemistry 51 4400-4403
Lehmann J Martin HL Lashley EL Marshall MW Judd JT (1986)Vitamin E in foods from high and low linoleic acid diets Journal ofAmerican Dietetic Association 86 1208-1216
Lehmann JW Putnam DH Qureshi AA (1994) Vitamin E isomers in grainamaranths (Amaranthus spp) Lipids 29 177-181
Leon J and Schwang KU (1992) Description and application of a screeningmethod to determine root morphology traits of cereals cultivars Journal ofAgronomy and Crop Science 169 128-134
Linares OF (2002) African rice (Oryza glaberrima) history and future potentialIn Proceedings of The National Academy of Science of the United States ofAmerica 9916360-16365
Ling WH Cheng QX MaJ Wang T (2001) Red and black rice decreaseatherosclerotic plaque formation and increase antioxidant status in rabbitsJournal of Nutrition 131 1421-1426
Linkohr BI Williamson LC Fitter AH Leyser O (2002) Nitrate andphosphate availability and distribution have different effects on root systemarchitecture of Arabidopsis Plant Journal 29751-760
Londo JP Chiang YC Hung KH Chiang TY Schaal BA (2006)Phylogeography of Asian wild rice Oryza rufipogon reveals multipleindependent domestications of cultivated rice Oryza sativa Proceedings ofThe National Academy of Science USA 103 9578-9583
Lu BR Naredo MEB Juliano AB Jackson MT (2000) Preliminary studieson taxonomy and biosystematics of the AA genome Oryza species
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(Poaceae) In Jacobs SW Everett LJ eds Grasses Systematics andEvolution CSIRO Melbourne pp51-58
Lynch JP and Brown KM (2008) Root strategies for phosphorus acquisition InWhite PJ Hammond JP TheEcophysiology of Plant ndashPhosphorusInteractions Netherlands Springer pp 83-116
Ma Z Bielenberg DG Brown KM Lynch JP (2001) Regulation of root hairdensity by phosphorus availability in Arabidopsis thaliana Plant CellEnviron 24 459-467
Maekawa M and Kita T (1984) The spectral characteristic of extraction pigmentof the genetic colouring grain in rice plants Hotsukaido universityagricultural faculty Farm Research Report 23 11-21
Mantegazza R Biloni M Grassi F Basso B Lu BR (2008) Temporal trendsof variation in Italian rice germplasm over the past two centuries revealed byAFLP and SSR markers Crop Science 481832-1840
Mccall MR and Frei B (1999) Can antioxidant vitamins materially reduceoxidative damage in humans Free Radical Biology and Medicine 261034-1053
Meng F Wei Y Yang X (2005) Iron content and bioavailability in rice Journalof Trace Element in Medicine and Biology 18 333-338
Messmer MM Melchinger AE Boppenmayer J Brunklaus-Jung E HermanRG (1992) Relationship among Early European Maize (Zea mays L)inbreds I Genetic Diversity among Flint and Dent Lines Revealed byRFLPs Crop Science 321301-1309
Mia MAB and Shamsuddin ZH(2011) Physio-morphological appraisal ofaromatic fine rice (Oryza sativa L) in relation to yield potentialInternational Journal of Botany 7 223-229
Miyazawa T Shibata A Sookwong P Kawakami Y Eitsuka T Asai AOikawa S Nakagawa K (2009) Antiangiogenic and anticancer potentialof unsaturated vitamin E (tocotrienol) The Journal of NutritionalBiochemistry 20 79-86
Molina J SikoraM Garud N Flowers JM Rubinstein S Reynolds AHuang P Jackson S Schaal BA Bustamante CD Boyko ARPurugganan MD (2011) Molecular evidence for a single evolutionaryorigin of domesticated rice PNAS 108 8351-8356
Mondini L Noorani A Pagnotta A (2009) Assessing plant genetic diversity bymolecular tools Diversity 1 19-35
Morgante M And Olivieri AM (1993) PCR- amplified microsatelites as markersin plant genetics Plant Journal 3 175-182
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Morishima H (2001) Evolution and domestication of rice In Khush GS BrarDS Hardy B eds RiceGenetics IV Proceedings of the FourthInternational Rice Genetics Symposium International Rice Research IntituteLos Banos Pp 63-77
Muntana N And Prasong S (2010) Study on total phenolic contents and theirantioxidant activities of thai white red and blck rice bran extracts PakistanJournal of Biological Sciences 13 170-174
Nesaretnam K (2008) Multitarget therapy of cancer by tocotrienols Cancerletters 269388-395
Norzaleha K Muhammad K Hamid AA S Mohamed Total phenolic contentsand antioxidant capacities of different coloured Malaysian rice grains Paperpresented at University Malaysia Terengganu Annual SymposiumTerengganu July 2012
Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
Oki T Masuda M Kobayashi M Nishiba Y Furuta S Suda I Sato T(2002) Polymeric procyanidins as radical- scavenging components in red-hulled rice Journal of Agricultural and Food Chemistry 50 7524-7529
Ong ASH (1993) Natural sources of tocotrienols In Packer L and Fuchs SVitamin E in Health and Disease New York Dekker pp 3-8
Oryza (2012) Malaysia Launches Project to Double Rice Output in 9 Yearshttpwwworyzacommalaysia-launches-project-double-rice-output-9-Accessed on 18 April 2013
OrsquoToole JC and Bland WL (1987) Genotypic variation in crop plant rootsystems Advance in Agronomy 4191-143
Panse VG and Sukhatme PV (1957) Genetics and Quantitative Characters inRelation to Plant Breeding Indian Journal Genetics 17 312-328
Peterson DM and Wood DF (1997) Composition and structure of high oil oatJournal of Cereal Science 26 121-128
Piironen V Syvaoja E-L Varo P Salminen K Koivistoinen P (1986)Tocopherols and tocotrienols in cereal products from Finland CerealChemistry 63 78-81
Peacuterez-Jimeacutenez J Arranz S Tabernero M Diaz-Rubio ME Serrano J GoniI Saura-Calixto F (2008) Updated methodology to determine antioxidantcapacity in plant foods oils and beverages Extraction measurement andexpression of results Food Research International 41 274-285
copy COPYRIG
HT UPM
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Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
copy COPYRIG
HT UPM
97
ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
copy COPYRIG
HT UPM
98
Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
copy COPYRIG
HT UPM
99
Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
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Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
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wild rice collected from Malaysia compared to cultivated rice MR 219Australian Journal of Crop Science 6 1502-1507
FinocchiaroF Ferrari B GianinettiA AstaCD Galaverna G ScazzinaFPellegrini N (2007) Characterization of antioxidant compounds of red andwhite rice and changes in total antioxidant capacity during processingMolecular Nutrition and Food Research 51(2007) 1006 ndash 1019
Forde B and Lorenzo H (2001) The nutritional control of root developmentPlant Soil 23251-68
Frei M and Becker K (2003) Studies on the in vitro starch digestibility and theglycemic index of six different indigenous rice cultivars from thePhilippines Food Chemistry 83 395-402
Fuentes JL Cornide MT Alvarez ASuarez E Borges E (2005) Geneticdiversity analysis of rice varieties (Oryza sativa L) based on morphologicalpedigree and DNA polymorphism data Plant Genetics Resources 3 353-359
Gahoonia TS amp Nielsen NE (2004) Root traits as tools for creating phosphorusefficient varieties Plant and Soil 260 47-57
El-Gammal MI and Shakour AA (2001) Emission of pollutant from harvest andburning of rice straw in Egypt villages (North East of Nile Delta) Journal ofUnion of Arab Biologist 15 191-206
Garris AJ Tai TH Coburn J Kresovich S McCouch S (2005) Geneticstructure and diversity in Oryza sativa L Genetics 169 1631-1638
Ge Zhang B Xian Chen Q Bo Luo S Yuan Zhang C Yang Q Dong Liu K(2012) Effect of NPK Defeciencies on Root Architetecture and Growth ofCucumber International Journal of Agriculture and Biology 14 145-148
Goffman FD and Bergman CJ (2004) Rice kernel phenolic content and itsrelationship with antiradical efficiency Journal of the Science of Food andAgriculture 84 1235-1240
Gramene (2006)Oryza taxonomy httpwwwgrameneorg Accessed on 20January 2013
Grams GW Blesin CW Inglett GE (1970) Distribution of tocopherols withinthe corn kernel Journal of the American Oil Chemistsrsquo Society 47337-339
Gupta PC and Orsquotoole JC (1986) Upland rice A global perspectiveInternational Rice Research Institute Los Banos Laguna Philippines POBox 933 Manila Philipines
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Hanafi MM Hartinie A Shukor J Mahmud TMM (2009) Upland ricevarieties in Malaysia agronomic and soil physico-chemical characteristicsPertanika Journal of Tropical Agricultural Science 32 225-246
HargroveT and Coffman WR (2006) Breeding history Rice Today 5 35-38
Hartinee A (2006) Increasing the yield of upland rice in idle land through nutrientand weed management Unpublished master dissertation University PutraMalaysia Malaysia
Harushima Y Yano M Shomura A Sato M Shimano T Kuboki YYamamoto T Lin SY Antonio BA Parco A Kajiya H Huang NYamamotoK Nagamura Y Kurata N Khush GS Sasaki T (1998) Ahigh density rice genetic linkage map with 2275 markers using a single F2population Genetics 148479-494
Holasova M (1997) Distribution of tocopherols and tocotrienols in the mainproducts of wheat and rye milling Czech Journal of Food Science 15 343-350
Holasova M Velisek J Davidek J (1995) Tocopherol and tocotrienol contentsin cereal grains Czech Journal of Food Science13 409-417
Hotz C and Brown KH (2004) Assessment of the risk of zinc dificiency inpopulations Food and Nutrition Bulletin 25 130-162
Hu C Zawistowski J Ling W Kitts DD (2003) Black rice (Oryza sativa Lindica) pigmented fraction suppresses both reactive oxygen species and nitricoxide in chemical and biological model systems Journal of Agricultural andFood Chemistry 51 5271-5277
Hu X Wang J Lu P Zhang H (2009) Assessment of Genetic Diversity inBroomcorn Millet (Panicum miliaceum L) using SSR markers Journal ofGenetics and Genomics 36 491-500
IRRI (2012) Sharing rice httpwwwirriorg Accessed on 18 December 2012
Islam MS Bhutya MSU Rahman S Hussain MM (2009) Evaluation ofSPAD and LCC Based Nitrogen Management in Rice (Oryza sativa L)Bangladesh Journal of Agriculture Research 34 661-672
Itani T And Ogawa M (2004) History and recent trends of red rice in JapanJapanese Journal of Crop Science 73 137-147
JhangT KaurM KaliaP and Sharma TR(2010) Efficiency of Different MarkerSystem for Molecular Characterization of Subtropical Carrot GermplasmJournal of Agriculture Science 148171-181
Jose LB Alfredo CR Luis HE (2003) The role of nutrient availability inregulating root architecture Current Opinion in Plant Biology 6280-287
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Johnson HW Robinson HP and Comstoc RE (1995) Estimation of Geneticand Environmental Variability in Soybeans Agronomy Journal 47314-318
Kang HW Cho YG Yoon UH Eun MY (1998) A Rapid DNA Extractionmethod for RFLP and PCR Analysis from a Single Dry Seed PlantMolecular Biology Reporter 161-9
Lai J Dey N Kim CS (2004) Characterization of the maize endospermtranscriptome and its comparison to the rice genome Genome Research 141932-1937
Lapitan VC Brar DS AbeT Redona ED (2007) Assessement of GeneticDiversity of Philippine Rice Cultivar Carrying Good Quality Traits usingSSR Markers Breeding Science 57263-270
Lee SC Kim JH Jeong SM Kim DR Ha JU Nam KC Ahn DU(2003) Effect of far-infrared radiation on the antioxidant activity of ricehulls Journal of Agricultural and Food Chemistry 51 4400-4403
Lehmann J Martin HL Lashley EL Marshall MW Judd JT (1986)Vitamin E in foods from high and low linoleic acid diets Journal ofAmerican Dietetic Association 86 1208-1216
Lehmann JW Putnam DH Qureshi AA (1994) Vitamin E isomers in grainamaranths (Amaranthus spp) Lipids 29 177-181
Leon J and Schwang KU (1992) Description and application of a screeningmethod to determine root morphology traits of cereals cultivars Journal ofAgronomy and Crop Science 169 128-134
Linares OF (2002) African rice (Oryza glaberrima) history and future potentialIn Proceedings of The National Academy of Science of the United States ofAmerica 9916360-16365
Ling WH Cheng QX MaJ Wang T (2001) Red and black rice decreaseatherosclerotic plaque formation and increase antioxidant status in rabbitsJournal of Nutrition 131 1421-1426
Linkohr BI Williamson LC Fitter AH Leyser O (2002) Nitrate andphosphate availability and distribution have different effects on root systemarchitecture of Arabidopsis Plant Journal 29751-760
Londo JP Chiang YC Hung KH Chiang TY Schaal BA (2006)Phylogeography of Asian wild rice Oryza rufipogon reveals multipleindependent domestications of cultivated rice Oryza sativa Proceedings ofThe National Academy of Science USA 103 9578-9583
Lu BR Naredo MEB Juliano AB Jackson MT (2000) Preliminary studieson taxonomy and biosystematics of the AA genome Oryza species
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(Poaceae) In Jacobs SW Everett LJ eds Grasses Systematics andEvolution CSIRO Melbourne pp51-58
Lynch JP and Brown KM (2008) Root strategies for phosphorus acquisition InWhite PJ Hammond JP TheEcophysiology of Plant ndashPhosphorusInteractions Netherlands Springer pp 83-116
Ma Z Bielenberg DG Brown KM Lynch JP (2001) Regulation of root hairdensity by phosphorus availability in Arabidopsis thaliana Plant CellEnviron 24 459-467
Maekawa M and Kita T (1984) The spectral characteristic of extraction pigmentof the genetic colouring grain in rice plants Hotsukaido universityagricultural faculty Farm Research Report 23 11-21
Mantegazza R Biloni M Grassi F Basso B Lu BR (2008) Temporal trendsof variation in Italian rice germplasm over the past two centuries revealed byAFLP and SSR markers Crop Science 481832-1840
Mccall MR and Frei B (1999) Can antioxidant vitamins materially reduceoxidative damage in humans Free Radical Biology and Medicine 261034-1053
Meng F Wei Y Yang X (2005) Iron content and bioavailability in rice Journalof Trace Element in Medicine and Biology 18 333-338
Messmer MM Melchinger AE Boppenmayer J Brunklaus-Jung E HermanRG (1992) Relationship among Early European Maize (Zea mays L)inbreds I Genetic Diversity among Flint and Dent Lines Revealed byRFLPs Crop Science 321301-1309
Mia MAB and Shamsuddin ZH(2011) Physio-morphological appraisal ofaromatic fine rice (Oryza sativa L) in relation to yield potentialInternational Journal of Botany 7 223-229
Miyazawa T Shibata A Sookwong P Kawakami Y Eitsuka T Asai AOikawa S Nakagawa K (2009) Antiangiogenic and anticancer potentialof unsaturated vitamin E (tocotrienol) The Journal of NutritionalBiochemistry 20 79-86
Molina J SikoraM Garud N Flowers JM Rubinstein S Reynolds AHuang P Jackson S Schaal BA Bustamante CD Boyko ARPurugganan MD (2011) Molecular evidence for a single evolutionaryorigin of domesticated rice PNAS 108 8351-8356
Mondini L Noorani A Pagnotta A (2009) Assessing plant genetic diversity bymolecular tools Diversity 1 19-35
Morgante M And Olivieri AM (1993) PCR- amplified microsatelites as markersin plant genetics Plant Journal 3 175-182
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Morishima H (2001) Evolution and domestication of rice In Khush GS BrarDS Hardy B eds RiceGenetics IV Proceedings of the FourthInternational Rice Genetics Symposium International Rice Research IntituteLos Banos Pp 63-77
Muntana N And Prasong S (2010) Study on total phenolic contents and theirantioxidant activities of thai white red and blck rice bran extracts PakistanJournal of Biological Sciences 13 170-174
Nesaretnam K (2008) Multitarget therapy of cancer by tocotrienols Cancerletters 269388-395
Norzaleha K Muhammad K Hamid AA S Mohamed Total phenolic contentsand antioxidant capacities of different coloured Malaysian rice grains Paperpresented at University Malaysia Terengganu Annual SymposiumTerengganu July 2012
Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
Oki T Masuda M Kobayashi M Nishiba Y Furuta S Suda I Sato T(2002) Polymeric procyanidins as radical- scavenging components in red-hulled rice Journal of Agricultural and Food Chemistry 50 7524-7529
Ong ASH (1993) Natural sources of tocotrienols In Packer L and Fuchs SVitamin E in Health and Disease New York Dekker pp 3-8
Oryza (2012) Malaysia Launches Project to Double Rice Output in 9 Yearshttpwwworyzacommalaysia-launches-project-double-rice-output-9-Accessed on 18 April 2013
OrsquoToole JC and Bland WL (1987) Genotypic variation in crop plant rootsystems Advance in Agronomy 4191-143
Panse VG and Sukhatme PV (1957) Genetics and Quantitative Characters inRelation to Plant Breeding Indian Journal Genetics 17 312-328
Peterson DM and Wood DF (1997) Composition and structure of high oil oatJournal of Cereal Science 26 121-128
Piironen V Syvaoja E-L Varo P Salminen K Koivistoinen P (1986)Tocopherols and tocotrienols in cereal products from Finland CerealChemistry 63 78-81
Peacuterez-Jimeacutenez J Arranz S Tabernero M Diaz-Rubio ME Serrano J GoniI Saura-Calixto F (2008) Updated methodology to determine antioxidantcapacity in plant foods oils and beverages Extraction measurement andexpression of results Food Research International 41 274-285
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Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
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ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
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Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
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Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
copy COPYRIG
HT UPM
100
Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
copy COPYRIG
HT UPM
92
Hanafi MM Hartinie A Shukor J Mahmud TMM (2009) Upland ricevarieties in Malaysia agronomic and soil physico-chemical characteristicsPertanika Journal of Tropical Agricultural Science 32 225-246
HargroveT and Coffman WR (2006) Breeding history Rice Today 5 35-38
Hartinee A (2006) Increasing the yield of upland rice in idle land through nutrientand weed management Unpublished master dissertation University PutraMalaysia Malaysia
Harushima Y Yano M Shomura A Sato M Shimano T Kuboki YYamamoto T Lin SY Antonio BA Parco A Kajiya H Huang NYamamotoK Nagamura Y Kurata N Khush GS Sasaki T (1998) Ahigh density rice genetic linkage map with 2275 markers using a single F2population Genetics 148479-494
Holasova M (1997) Distribution of tocopherols and tocotrienols in the mainproducts of wheat and rye milling Czech Journal of Food Science 15 343-350
Holasova M Velisek J Davidek J (1995) Tocopherol and tocotrienol contentsin cereal grains Czech Journal of Food Science13 409-417
Hotz C and Brown KH (2004) Assessment of the risk of zinc dificiency inpopulations Food and Nutrition Bulletin 25 130-162
Hu C Zawistowski J Ling W Kitts DD (2003) Black rice (Oryza sativa Lindica) pigmented fraction suppresses both reactive oxygen species and nitricoxide in chemical and biological model systems Journal of Agricultural andFood Chemistry 51 5271-5277
Hu X Wang J Lu P Zhang H (2009) Assessment of Genetic Diversity inBroomcorn Millet (Panicum miliaceum L) using SSR markers Journal ofGenetics and Genomics 36 491-500
IRRI (2012) Sharing rice httpwwwirriorg Accessed on 18 December 2012
Islam MS Bhutya MSU Rahman S Hussain MM (2009) Evaluation ofSPAD and LCC Based Nitrogen Management in Rice (Oryza sativa L)Bangladesh Journal of Agriculture Research 34 661-672
Itani T And Ogawa M (2004) History and recent trends of red rice in JapanJapanese Journal of Crop Science 73 137-147
JhangT KaurM KaliaP and Sharma TR(2010) Efficiency of Different MarkerSystem for Molecular Characterization of Subtropical Carrot GermplasmJournal of Agriculture Science 148171-181
Jose LB Alfredo CR Luis HE (2003) The role of nutrient availability inregulating root architecture Current Opinion in Plant Biology 6280-287
copy COPYRIG
HT UPM
93
Johnson HW Robinson HP and Comstoc RE (1995) Estimation of Geneticand Environmental Variability in Soybeans Agronomy Journal 47314-318
Kang HW Cho YG Yoon UH Eun MY (1998) A Rapid DNA Extractionmethod for RFLP and PCR Analysis from a Single Dry Seed PlantMolecular Biology Reporter 161-9
Lai J Dey N Kim CS (2004) Characterization of the maize endospermtranscriptome and its comparison to the rice genome Genome Research 141932-1937
Lapitan VC Brar DS AbeT Redona ED (2007) Assessement of GeneticDiversity of Philippine Rice Cultivar Carrying Good Quality Traits usingSSR Markers Breeding Science 57263-270
Lee SC Kim JH Jeong SM Kim DR Ha JU Nam KC Ahn DU(2003) Effect of far-infrared radiation on the antioxidant activity of ricehulls Journal of Agricultural and Food Chemistry 51 4400-4403
Lehmann J Martin HL Lashley EL Marshall MW Judd JT (1986)Vitamin E in foods from high and low linoleic acid diets Journal ofAmerican Dietetic Association 86 1208-1216
Lehmann JW Putnam DH Qureshi AA (1994) Vitamin E isomers in grainamaranths (Amaranthus spp) Lipids 29 177-181
Leon J and Schwang KU (1992) Description and application of a screeningmethod to determine root morphology traits of cereals cultivars Journal ofAgronomy and Crop Science 169 128-134
Linares OF (2002) African rice (Oryza glaberrima) history and future potentialIn Proceedings of The National Academy of Science of the United States ofAmerica 9916360-16365
Ling WH Cheng QX MaJ Wang T (2001) Red and black rice decreaseatherosclerotic plaque formation and increase antioxidant status in rabbitsJournal of Nutrition 131 1421-1426
Linkohr BI Williamson LC Fitter AH Leyser O (2002) Nitrate andphosphate availability and distribution have different effects on root systemarchitecture of Arabidopsis Plant Journal 29751-760
Londo JP Chiang YC Hung KH Chiang TY Schaal BA (2006)Phylogeography of Asian wild rice Oryza rufipogon reveals multipleindependent domestications of cultivated rice Oryza sativa Proceedings ofThe National Academy of Science USA 103 9578-9583
Lu BR Naredo MEB Juliano AB Jackson MT (2000) Preliminary studieson taxonomy and biosystematics of the AA genome Oryza species
copy COPYRIG
HT UPM
94
(Poaceae) In Jacobs SW Everett LJ eds Grasses Systematics andEvolution CSIRO Melbourne pp51-58
Lynch JP and Brown KM (2008) Root strategies for phosphorus acquisition InWhite PJ Hammond JP TheEcophysiology of Plant ndashPhosphorusInteractions Netherlands Springer pp 83-116
Ma Z Bielenberg DG Brown KM Lynch JP (2001) Regulation of root hairdensity by phosphorus availability in Arabidopsis thaliana Plant CellEnviron 24 459-467
Maekawa M and Kita T (1984) The spectral characteristic of extraction pigmentof the genetic colouring grain in rice plants Hotsukaido universityagricultural faculty Farm Research Report 23 11-21
Mantegazza R Biloni M Grassi F Basso B Lu BR (2008) Temporal trendsof variation in Italian rice germplasm over the past two centuries revealed byAFLP and SSR markers Crop Science 481832-1840
Mccall MR and Frei B (1999) Can antioxidant vitamins materially reduceoxidative damage in humans Free Radical Biology and Medicine 261034-1053
Meng F Wei Y Yang X (2005) Iron content and bioavailability in rice Journalof Trace Element in Medicine and Biology 18 333-338
Messmer MM Melchinger AE Boppenmayer J Brunklaus-Jung E HermanRG (1992) Relationship among Early European Maize (Zea mays L)inbreds I Genetic Diversity among Flint and Dent Lines Revealed byRFLPs Crop Science 321301-1309
Mia MAB and Shamsuddin ZH(2011) Physio-morphological appraisal ofaromatic fine rice (Oryza sativa L) in relation to yield potentialInternational Journal of Botany 7 223-229
Miyazawa T Shibata A Sookwong P Kawakami Y Eitsuka T Asai AOikawa S Nakagawa K (2009) Antiangiogenic and anticancer potentialof unsaturated vitamin E (tocotrienol) The Journal of NutritionalBiochemistry 20 79-86
Molina J SikoraM Garud N Flowers JM Rubinstein S Reynolds AHuang P Jackson S Schaal BA Bustamante CD Boyko ARPurugganan MD (2011) Molecular evidence for a single evolutionaryorigin of domesticated rice PNAS 108 8351-8356
Mondini L Noorani A Pagnotta A (2009) Assessing plant genetic diversity bymolecular tools Diversity 1 19-35
Morgante M And Olivieri AM (1993) PCR- amplified microsatelites as markersin plant genetics Plant Journal 3 175-182
copy COPYRIG
HT UPM
95
Morishima H (2001) Evolution and domestication of rice In Khush GS BrarDS Hardy B eds RiceGenetics IV Proceedings of the FourthInternational Rice Genetics Symposium International Rice Research IntituteLos Banos Pp 63-77
Muntana N And Prasong S (2010) Study on total phenolic contents and theirantioxidant activities of thai white red and blck rice bran extracts PakistanJournal of Biological Sciences 13 170-174
Nesaretnam K (2008) Multitarget therapy of cancer by tocotrienols Cancerletters 269388-395
Norzaleha K Muhammad K Hamid AA S Mohamed Total phenolic contentsand antioxidant capacities of different coloured Malaysian rice grains Paperpresented at University Malaysia Terengganu Annual SymposiumTerengganu July 2012
Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
Oki T Masuda M Kobayashi M Nishiba Y Furuta S Suda I Sato T(2002) Polymeric procyanidins as radical- scavenging components in red-hulled rice Journal of Agricultural and Food Chemistry 50 7524-7529
Ong ASH (1993) Natural sources of tocotrienols In Packer L and Fuchs SVitamin E in Health and Disease New York Dekker pp 3-8
Oryza (2012) Malaysia Launches Project to Double Rice Output in 9 Yearshttpwwworyzacommalaysia-launches-project-double-rice-output-9-Accessed on 18 April 2013
OrsquoToole JC and Bland WL (1987) Genotypic variation in crop plant rootsystems Advance in Agronomy 4191-143
Panse VG and Sukhatme PV (1957) Genetics and Quantitative Characters inRelation to Plant Breeding Indian Journal Genetics 17 312-328
Peterson DM and Wood DF (1997) Composition and structure of high oil oatJournal of Cereal Science 26 121-128
Piironen V Syvaoja E-L Varo P Salminen K Koivistoinen P (1986)Tocopherols and tocotrienols in cereal products from Finland CerealChemistry 63 78-81
Peacuterez-Jimeacutenez J Arranz S Tabernero M Diaz-Rubio ME Serrano J GoniI Saura-Calixto F (2008) Updated methodology to determine antioxidantcapacity in plant foods oils and beverages Extraction measurement andexpression of results Food Research International 41 274-285
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Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
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ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
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Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
copy COPYRIG
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Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
copy COPYRIG
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Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
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Johnson HW Robinson HP and Comstoc RE (1995) Estimation of Geneticand Environmental Variability in Soybeans Agronomy Journal 47314-318
Kang HW Cho YG Yoon UH Eun MY (1998) A Rapid DNA Extractionmethod for RFLP and PCR Analysis from a Single Dry Seed PlantMolecular Biology Reporter 161-9
Lai J Dey N Kim CS (2004) Characterization of the maize endospermtranscriptome and its comparison to the rice genome Genome Research 141932-1937
Lapitan VC Brar DS AbeT Redona ED (2007) Assessement of GeneticDiversity of Philippine Rice Cultivar Carrying Good Quality Traits usingSSR Markers Breeding Science 57263-270
Lee SC Kim JH Jeong SM Kim DR Ha JU Nam KC Ahn DU(2003) Effect of far-infrared radiation on the antioxidant activity of ricehulls Journal of Agricultural and Food Chemistry 51 4400-4403
Lehmann J Martin HL Lashley EL Marshall MW Judd JT (1986)Vitamin E in foods from high and low linoleic acid diets Journal ofAmerican Dietetic Association 86 1208-1216
Lehmann JW Putnam DH Qureshi AA (1994) Vitamin E isomers in grainamaranths (Amaranthus spp) Lipids 29 177-181
Leon J and Schwang KU (1992) Description and application of a screeningmethod to determine root morphology traits of cereals cultivars Journal ofAgronomy and Crop Science 169 128-134
Linares OF (2002) African rice (Oryza glaberrima) history and future potentialIn Proceedings of The National Academy of Science of the United States ofAmerica 9916360-16365
Ling WH Cheng QX MaJ Wang T (2001) Red and black rice decreaseatherosclerotic plaque formation and increase antioxidant status in rabbitsJournal of Nutrition 131 1421-1426
Linkohr BI Williamson LC Fitter AH Leyser O (2002) Nitrate andphosphate availability and distribution have different effects on root systemarchitecture of Arabidopsis Plant Journal 29751-760
Londo JP Chiang YC Hung KH Chiang TY Schaal BA (2006)Phylogeography of Asian wild rice Oryza rufipogon reveals multipleindependent domestications of cultivated rice Oryza sativa Proceedings ofThe National Academy of Science USA 103 9578-9583
Lu BR Naredo MEB Juliano AB Jackson MT (2000) Preliminary studieson taxonomy and biosystematics of the AA genome Oryza species
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(Poaceae) In Jacobs SW Everett LJ eds Grasses Systematics andEvolution CSIRO Melbourne pp51-58
Lynch JP and Brown KM (2008) Root strategies for phosphorus acquisition InWhite PJ Hammond JP TheEcophysiology of Plant ndashPhosphorusInteractions Netherlands Springer pp 83-116
Ma Z Bielenberg DG Brown KM Lynch JP (2001) Regulation of root hairdensity by phosphorus availability in Arabidopsis thaliana Plant CellEnviron 24 459-467
Maekawa M and Kita T (1984) The spectral characteristic of extraction pigmentof the genetic colouring grain in rice plants Hotsukaido universityagricultural faculty Farm Research Report 23 11-21
Mantegazza R Biloni M Grassi F Basso B Lu BR (2008) Temporal trendsof variation in Italian rice germplasm over the past two centuries revealed byAFLP and SSR markers Crop Science 481832-1840
Mccall MR and Frei B (1999) Can antioxidant vitamins materially reduceoxidative damage in humans Free Radical Biology and Medicine 261034-1053
Meng F Wei Y Yang X (2005) Iron content and bioavailability in rice Journalof Trace Element in Medicine and Biology 18 333-338
Messmer MM Melchinger AE Boppenmayer J Brunklaus-Jung E HermanRG (1992) Relationship among Early European Maize (Zea mays L)inbreds I Genetic Diversity among Flint and Dent Lines Revealed byRFLPs Crop Science 321301-1309
Mia MAB and Shamsuddin ZH(2011) Physio-morphological appraisal ofaromatic fine rice (Oryza sativa L) in relation to yield potentialInternational Journal of Botany 7 223-229
Miyazawa T Shibata A Sookwong P Kawakami Y Eitsuka T Asai AOikawa S Nakagawa K (2009) Antiangiogenic and anticancer potentialof unsaturated vitamin E (tocotrienol) The Journal of NutritionalBiochemistry 20 79-86
Molina J SikoraM Garud N Flowers JM Rubinstein S Reynolds AHuang P Jackson S Schaal BA Bustamante CD Boyko ARPurugganan MD (2011) Molecular evidence for a single evolutionaryorigin of domesticated rice PNAS 108 8351-8356
Mondini L Noorani A Pagnotta A (2009) Assessing plant genetic diversity bymolecular tools Diversity 1 19-35
Morgante M And Olivieri AM (1993) PCR- amplified microsatelites as markersin plant genetics Plant Journal 3 175-182
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Morishima H (2001) Evolution and domestication of rice In Khush GS BrarDS Hardy B eds RiceGenetics IV Proceedings of the FourthInternational Rice Genetics Symposium International Rice Research IntituteLos Banos Pp 63-77
Muntana N And Prasong S (2010) Study on total phenolic contents and theirantioxidant activities of thai white red and blck rice bran extracts PakistanJournal of Biological Sciences 13 170-174
Nesaretnam K (2008) Multitarget therapy of cancer by tocotrienols Cancerletters 269388-395
Norzaleha K Muhammad K Hamid AA S Mohamed Total phenolic contentsand antioxidant capacities of different coloured Malaysian rice grains Paperpresented at University Malaysia Terengganu Annual SymposiumTerengganu July 2012
Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
Oki T Masuda M Kobayashi M Nishiba Y Furuta S Suda I Sato T(2002) Polymeric procyanidins as radical- scavenging components in red-hulled rice Journal of Agricultural and Food Chemistry 50 7524-7529
Ong ASH (1993) Natural sources of tocotrienols In Packer L and Fuchs SVitamin E in Health and Disease New York Dekker pp 3-8
Oryza (2012) Malaysia Launches Project to Double Rice Output in 9 Yearshttpwwworyzacommalaysia-launches-project-double-rice-output-9-Accessed on 18 April 2013
OrsquoToole JC and Bland WL (1987) Genotypic variation in crop plant rootsystems Advance in Agronomy 4191-143
Panse VG and Sukhatme PV (1957) Genetics and Quantitative Characters inRelation to Plant Breeding Indian Journal Genetics 17 312-328
Peterson DM and Wood DF (1997) Composition and structure of high oil oatJournal of Cereal Science 26 121-128
Piironen V Syvaoja E-L Varo P Salminen K Koivistoinen P (1986)Tocopherols and tocotrienols in cereal products from Finland CerealChemistry 63 78-81
Peacuterez-Jimeacutenez J Arranz S Tabernero M Diaz-Rubio ME Serrano J GoniI Saura-Calixto F (2008) Updated methodology to determine antioxidantcapacity in plant foods oils and beverages Extraction measurement andexpression of results Food Research International 41 274-285
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Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
copy COPYRIG
HT UPM
97
ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
copy COPYRIG
HT UPM
98
Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
copy COPYRIG
HT UPM
99
Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
copy COPYRIG
HT UPM
100
Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
copy COPYRIG
HT UPM
94
(Poaceae) In Jacobs SW Everett LJ eds Grasses Systematics andEvolution CSIRO Melbourne pp51-58
Lynch JP and Brown KM (2008) Root strategies for phosphorus acquisition InWhite PJ Hammond JP TheEcophysiology of Plant ndashPhosphorusInteractions Netherlands Springer pp 83-116
Ma Z Bielenberg DG Brown KM Lynch JP (2001) Regulation of root hairdensity by phosphorus availability in Arabidopsis thaliana Plant CellEnviron 24 459-467
Maekawa M and Kita T (1984) The spectral characteristic of extraction pigmentof the genetic colouring grain in rice plants Hotsukaido universityagricultural faculty Farm Research Report 23 11-21
Mantegazza R Biloni M Grassi F Basso B Lu BR (2008) Temporal trendsof variation in Italian rice germplasm over the past two centuries revealed byAFLP and SSR markers Crop Science 481832-1840
Mccall MR and Frei B (1999) Can antioxidant vitamins materially reduceoxidative damage in humans Free Radical Biology and Medicine 261034-1053
Meng F Wei Y Yang X (2005) Iron content and bioavailability in rice Journalof Trace Element in Medicine and Biology 18 333-338
Messmer MM Melchinger AE Boppenmayer J Brunklaus-Jung E HermanRG (1992) Relationship among Early European Maize (Zea mays L)inbreds I Genetic Diversity among Flint and Dent Lines Revealed byRFLPs Crop Science 321301-1309
Mia MAB and Shamsuddin ZH(2011) Physio-morphological appraisal ofaromatic fine rice (Oryza sativa L) in relation to yield potentialInternational Journal of Botany 7 223-229
Miyazawa T Shibata A Sookwong P Kawakami Y Eitsuka T Asai AOikawa S Nakagawa K (2009) Antiangiogenic and anticancer potentialof unsaturated vitamin E (tocotrienol) The Journal of NutritionalBiochemistry 20 79-86
Molina J SikoraM Garud N Flowers JM Rubinstein S Reynolds AHuang P Jackson S Schaal BA Bustamante CD Boyko ARPurugganan MD (2011) Molecular evidence for a single evolutionaryorigin of domesticated rice PNAS 108 8351-8356
Mondini L Noorani A Pagnotta A (2009) Assessing plant genetic diversity bymolecular tools Diversity 1 19-35
Morgante M And Olivieri AM (1993) PCR- amplified microsatelites as markersin plant genetics Plant Journal 3 175-182
copy COPYRIG
HT UPM
95
Morishima H (2001) Evolution and domestication of rice In Khush GS BrarDS Hardy B eds RiceGenetics IV Proceedings of the FourthInternational Rice Genetics Symposium International Rice Research IntituteLos Banos Pp 63-77
Muntana N And Prasong S (2010) Study on total phenolic contents and theirantioxidant activities of thai white red and blck rice bran extracts PakistanJournal of Biological Sciences 13 170-174
Nesaretnam K (2008) Multitarget therapy of cancer by tocotrienols Cancerletters 269388-395
Norzaleha K Muhammad K Hamid AA S Mohamed Total phenolic contentsand antioxidant capacities of different coloured Malaysian rice grains Paperpresented at University Malaysia Terengganu Annual SymposiumTerengganu July 2012
Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
Oki T Masuda M Kobayashi M Nishiba Y Furuta S Suda I Sato T(2002) Polymeric procyanidins as radical- scavenging components in red-hulled rice Journal of Agricultural and Food Chemistry 50 7524-7529
Ong ASH (1993) Natural sources of tocotrienols In Packer L and Fuchs SVitamin E in Health and Disease New York Dekker pp 3-8
Oryza (2012) Malaysia Launches Project to Double Rice Output in 9 Yearshttpwwworyzacommalaysia-launches-project-double-rice-output-9-Accessed on 18 April 2013
OrsquoToole JC and Bland WL (1987) Genotypic variation in crop plant rootsystems Advance in Agronomy 4191-143
Panse VG and Sukhatme PV (1957) Genetics and Quantitative Characters inRelation to Plant Breeding Indian Journal Genetics 17 312-328
Peterson DM and Wood DF (1997) Composition and structure of high oil oatJournal of Cereal Science 26 121-128
Piironen V Syvaoja E-L Varo P Salminen K Koivistoinen P (1986)Tocopherols and tocotrienols in cereal products from Finland CerealChemistry 63 78-81
Peacuterez-Jimeacutenez J Arranz S Tabernero M Diaz-Rubio ME Serrano J GoniI Saura-Calixto F (2008) Updated methodology to determine antioxidantcapacity in plant foods oils and beverages Extraction measurement andexpression of results Food Research International 41 274-285
copy COPYRIG
HT UPM
96
Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
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ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
copy COPYRIG
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Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
copy COPYRIG
HT UPM
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Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
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Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
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Morishima H (2001) Evolution and domestication of rice In Khush GS BrarDS Hardy B eds RiceGenetics IV Proceedings of the FourthInternational Rice Genetics Symposium International Rice Research IntituteLos Banos Pp 63-77
Muntana N And Prasong S (2010) Study on total phenolic contents and theirantioxidant activities of thai white red and blck rice bran extracts PakistanJournal of Biological Sciences 13 170-174
Nesaretnam K (2008) Multitarget therapy of cancer by tocotrienols Cancerletters 269388-395
Norzaleha K Muhammad K Hamid AA S Mohamed Total phenolic contentsand antioxidant capacities of different coloured Malaysian rice grains Paperpresented at University Malaysia Terengganu Annual SymposiumTerengganu July 2012
Oka HI (1988) Origin of cultivated rice Elsevier Amsterdam pp 254
Oki T Masuda M Kobayashi M Nishiba Y Furuta S Suda I Sato T(2002) Polymeric procyanidins as radical- scavenging components in red-hulled rice Journal of Agricultural and Food Chemistry 50 7524-7529
Ong ASH (1993) Natural sources of tocotrienols In Packer L and Fuchs SVitamin E in Health and Disease New York Dekker pp 3-8
Oryza (2012) Malaysia Launches Project to Double Rice Output in 9 Yearshttpwwworyzacommalaysia-launches-project-double-rice-output-9-Accessed on 18 April 2013
OrsquoToole JC and Bland WL (1987) Genotypic variation in crop plant rootsystems Advance in Agronomy 4191-143
Panse VG and Sukhatme PV (1957) Genetics and Quantitative Characters inRelation to Plant Breeding Indian Journal Genetics 17 312-328
Peterson DM and Wood DF (1997) Composition and structure of high oil oatJournal of Cereal Science 26 121-128
Piironen V Syvaoja E-L Varo P Salminen K Koivistoinen P (1986)Tocopherols and tocotrienols in cereal products from Finland CerealChemistry 63 78-81
Peacuterez-Jimeacutenez J Arranz S Tabernero M Diaz-Rubio ME Serrano J GoniI Saura-Calixto F (2008) Updated methodology to determine antioxidantcapacity in plant foods oils and beverages Extraction measurement andexpression of results Food Research International 41 274-285
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Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
copy COPYRIG
HT UPM
97
ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
copy COPYRIG
HT UPM
98
Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
copy COPYRIG
HT UPM
99
Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
copy COPYRIG
HT UPM
100
Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
copy COPYRIG
HT UPM
96
Qi YW Zhang DL Zhang HL Wang MX Sun JL Wei XH Qiu ZETang SX Cao YS Wang XK Li ZC (2006) Genetic diversity od ricecultivars (OSativa L) in China and the temporal trends in recent fifty yearsChinese Science Bulletin 51 681-688
Rahman S Sharma MP Sahai S (2006) Nutritional and medicinal values ofsome indigineous rice varieties Indian Journal of Traditional Knowledge 5454-458
Rajeev KV Lekha P Junichi K Pooron MG Krishnamurthy L Dave H(2011) Genomics and physiological approaches for root trait breeding toimprove drought tolerance in Chickpea (Cicar ariatinum L) Root Genomics10233-250
Ramaiah K and Rao MVBN (1953) Rice Breeding and Genetics ICAR ScienceMonograph 19 Indian Council of Agricultural Research New Delhi India
RaviM Geethahanjali S Sameeyafarheen F Maheswaran M (2003) MolecularMarker based Genetic Diversity Analysis in Rice (Oryza sativa L) usingRAPD and SSR markers Euphytica 133 243ndash252
Ricciarelli R Zing JM Nazi A (2002) The 80th anniversary of vitamin Ebeyond its antioxidant properties Biological Chemistry 383 457-465
Rosenberg M (2012) Current world population httpgeographyaboutcomAccessed on 3 February 2013
Rosta K (1975) Variety determination in rice Seed Science and Technology3161-168
Ryu SN Park SZ Ho CT (1998) High performance liquid chromatographicdetermination of anthocyanin pigments in some varieties of black riceJournal of Food and Drug Analysis 6 729-736
Samadia DK (2005) Genetic Variability Studies in Lasora (Cordia myxa Roxb)Indian Journal Plant genetics Resources 18 236-240
Schroeder MT Becker EM Skibsted LH (2006) Molecular mechanism ofantioxidant synergism of tocotrienols and carotenoids in palm oil Journal ofAgriculture and Food Chemistry 543445ndash3453
Seedek SEM Hammoud SAA Ammar MH Metwally TF (2009) GeneticVariability Heritability Genetic Advance Andd Cluster Analysis for SomePhysiological Traits and Grain Yield And Its Components in Rice (Oryzasativa L) Journal of Agriculture Resource 35 858-877
Seppanen CM Song Q and Csallany AS 2010 The antioxidant functions oftocopherol and tocotrienol homologues in oils fats and food systemsJournal of the American Oil Chemists Society 87 469-481
copy COPYRIG
HT UPM
97
ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
copy COPYRIG
HT UPM
98
Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
copy COPYRIG
HT UPM
99
Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
copy COPYRIG
HT UPM
100
Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
copy COPYRIG
HT UPM
97
ShahnawazM Sheikh SA Bhangar MI Ahmed E (2010) Total phenoliccompounds and antioxidants activity of jamun fruit (Eugenia jambolona)products Pakistan Journal of Food Science 2031-41
Sharma SD Tripathy S Biswal J (2000) Origin of Oryza sativa and itsecotypes In Nanda JS Rice Breeding and Genentics Research Prioritiesand Challenges Science Publication Enfield
Singh SK Singh CM Lal GM (2011) Assessement of Genetic Variability forYields and Its Component Characters in Rice (Oryza sativa L) Research inPlant Biology 173-76
Singh RK Singh US Kush GS (2000) Aromatic rices New Delhi Oxfordand IBH publishing
Sirajul M (2013) Genetic divergence of rice genotypes resistant to bacterial blightrevealed by quantitative traits and molecular markers Unpublished masterdissertation University Putra Malaysia Malaysia
Sohrabi M Rafii MY Hanafi MM Siti Nor Akmar A Latif MA (2012)Genetic Diversity of Upland Rice Germplasm in Malaysia Based onQuantitative Traits The Scientific World Journal 6175-182
Sood DR Deka SC Singh AP (2006) Nutritional quality of basmati ricegenotypes Journal of Dairying Foods and Home Science 25 1-7
Sookwong P Murata K Nakagawa K Shibata A Kimura T Yamaguchi MKojima Y Miyazawa T (2009) Cross-fertilization for enhancingtocotrienol biosynthesis in rice plants anf QTL analysis of their F2 progeniesJournal of Agriculture and Food Chemistry 57 4620-4625
Sun CQ Wang K Li ZC Yoshimura A Iwata N (2001) Comparison of thegenetic diversity common wild rice (Oryza rufipogon Griff) and cultivatedrice (Oryza sativa L) using RFLP markers Theoretical and AppliedGenetics 102 157-162
Surek H and Beser N (2003) Selection for grain yield and yield components inearly generations for temperate rice Philippine Journal of Crop Science 283-15
Suzuki M Kimur T Yamagishi K Shinmoto H Yamak K (2004) Comparisonof Mineral Contents in 8 cultivars of Pigmented Brown Rice Journal of theJapanese Society for Food Science and Technology51 424-427
Sompong R Ehn SS Martin GL Berghofer E (2011) Physicochemical andantioxidative properties of red and black rice varieties from Thailand Chinaand Sri Lanka Food Chemitry 124132-140
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Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
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Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
copy COPYRIG
HT UPM
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Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
copy COPYRIG
HT UPM
98
Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L In Tsunoda STakahashi N eds Biology of rice Elsevier Amsterdam pp 31-67
Tari DB Gazanchian A Pirdashti HA Nasiri M (2009) Flag leafmorphophysiological response to different agronomical treatments in apromising line of rice American-Eurasian Journal of Agriculture andEnvironment Science 5403-408
Teo YH Beyrouty CA Norman RJ Gbur EE (1995) Nutrient uptakerelationship to root characteristics of rice Plant and Soil 171 297-302
Tsaknis J Lalas S Gergis V Dourtoglou V Spiliotis V (1999)Characterization of Moringa oleifera Variety Mbololo Seed Oil of KenyaJournal of Agricultural and Food Chemistry 47 4495-4499
Uga Y Ebana K Abe J Morita S Okuno K Yano M (2009) Variation inroot morphology and anatomy among accessions of cultivated rice (Oryzasativa L) with different genetic backgrounds Breeding Science 59 87-93
Upadhyay P Singh VK Neeraja CN (2011) Identification of GenotypeSpecific Alleles and Molecular Diversity Assessement of Popular Rice(Oryza Sativa L) Varieties of India International Journal of Plant Breedingand Genetics5 130-140
Ullstrup AJ (1972) The impacts of the southern corn leaf blight epidemics of1970-1971 Annual Review of Phytopathology 10 37-50
Vlahov G Chepkwony PK Ndalut PK (2002) (13)C NMR characterization oftriacylglycerols of Moringa oleifera seed oil an oleic-vaccenic acid oilJournal of Agricultural and Food Chemistry 50 970-975
Walter M and Marchesan E (2011) Phenolic compunds and antioxidants activityof rice Brazilian Archives of Biology and Technology54 371-377
Wang Y Mi GH Chen FJ Zhang JH Zhang FS (2004) Response of rootmorphology to nitrate supply and its contribution to nitrogen accumulation inmaize Journal of Plant Nutrition 272189-2202
Wang L Newman RK Newman CW Jackson LL Hofer PJ (1993)Tocotrienol and fatty acid composition of barley oil and their effects on lipidmetabolism Plant Foods for Human Nutrition 439-17
Wei X Yuan X Yu H Wang Y Xu Q(2009) Temporal changes in SSRallelic diversity of major rice cultivars in China Journal of Genetics andGenomics 36 363ndash37
WHO (2002) The World Health Report 2002 GenevaWHO
copy COPYRIG
HT UPM
99
Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
copy COPYRIG
HT UPM
100
Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
copy COPYRIG
HT UPM
99
Wong SC Yiu PH Bong STW Lee HH Neoh PNP Rajan A (2009)Analysis of Sarawak bario rice diversity using microsatelite markersAmerican Journal of Agrucultural and Biological Sciences 4 298-304
Yamanaka S Jatoi SA Yi SS Kothari SL Htut T Watnabe KN (2011)Genetic diversity of Myanmar rice and their implementation on managementmethods African Journal of Biotechnology 10 1290-1298
Yafang S Gan Z Jinsong B (2011) Total phenolic content and antioxidantcapacity of rice grains with extremely small size African Journal ofAgricultural Research 6 2289-2293
Yang W Peng S Laza RC Vispers RM Sese MLD (2007) Grain yield andyield attributes of new plant type and hybrid rice Crop Science 47 1393-1400
Ya-wen Z Jia-fu L Lu-xiang W Shi quan S Zi-Chao L Xiangkun W Guo-song W Zhong-yi Y (2004) Analysis on mineral contents in associatedwith varietal type in core collection of Yunnan rice Rice Science 11 106-112
Zafar N Aziz S Masood S (2006) Phenotypic Divergence for Agro-Morphological Traits among Landrace Genotypes of Rice (Oryza sativa L)from Pakistan International Journal of Agriculture and Biology 6 335-339
Zapico L FC Namocatcat JA Turner JLC (2010) Genetic Diversity Analysisof Traditional Upland Rice Cultivars in Kihan Malapatan SaranganiProvince Philippines Using Morphometric Markers Philippine Journal ofScience139177-180
Zeng YW Liu JF Wang LX Du J Pu XY Yang SM (2006)Ecogeographic difference and variation pattern of mineral contents forYunnan rice landracesActa Agronimica Sinica 32 1166ndash1173
Zhang BG Chen QX Luo SB Zhang CY Yang Q Liu KD (2012)Effects of NPK deficiencies on root architecture and growth of cucumberInternational Journal of Agriculture and Biology14 145-148
Zhang H and Forde B (1998) An Arabidopsis MADS box gene that controlnutrient-induced changes in root architecture Science 279407-409
Zhang MW Guo BJ Zhang RF Chi JW Wei ZC (2006) Separationpurification and identification of antioxidant compositions in black riceAgricultural Science China 5 431-440
Zhu J Mickelson SM Kaepler SM Lynch JP (2006) Detection ofquantitative trait loci for seminal root traits in maize (Zea mays L) seedlingsgrown under differential phosphorus levels Theoretical and AppliedGenetics 1131-10
copy COPYRIG
HT UPM
100
Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622
copy COPYRIG
HT UPM
100
Zhu Q Zheng X Luo J Gaut BS Ge S (2007) Multilocus analysis ofnucleotide variation of Oryza sativa and its wild relatives severe bottleneckduring domestication of rice Molecular Biology and Evolution 24 857-888
Zubair M Anwar F Ashraf M Uddin MK (2012) Characterization of high ndashvalue bioactives in some selected varieties of Pakistani rice InternationalJournal of Molecular Science 13 4608-4622