Applied Genomic Research in Rice Applied Genomic Research in Rice Genetic ImprovementGenetic Improvement

Lokesh Gour & Lakshman GuptaGuided by:-Guided by:-Dr. S.K. Singh, Assistant Professor Dr. S.K. Singh, Assistant Professor JNKVV, JabalpurJNKVV, Jabalpur

DEPARTMENT OF PLANT BREEDING & GENETICS DEPARTMENT OF PLANT BREEDING & GENETICS JAWAHARLAL NEHRU KRISHI VISHWA VIDYALAYA JAWAHARLAL NEHRU KRISHI VISHWA VIDYALAYA

JABALPUR (M.P.)JABALPUR (M.P.)

CONTENTS

1.Introduction

2.Genomics

3.Need of Genomic research in rice

4.Conventional to molecular breeding through genomic research

5.5.Laboratories for genomic research in India Laboratories for genomic research in India

6.Tools for Genomic research

7.Technologies for implication of genomics

8.Application areas of genomics research

9.Current status

10.Examples of implication of genomics

11.Conclusion

12. Some of References

INTRODUCTION Rice is the world’s most important food crop and a staple food for more

than half of the world’s population. More than 90% of the world’s rice is produced and consumed in Asia, where 60% of the people live.

In the last six decades, rice production has steadily kept in pace with the population growth rate, mainly due to the gains from the technologies of green revolution era such as semi – dwarf, fertilizer responsive high yielding varieties and other associated managerial technologies.

Rice is a model crop for genetics and breeding research:-

1. Small genomic size – 45 × 10⁶ bp.2. Gene bank with 1,00,000 accessions.3. Highly dense molecular map.4. Several wild species.5. Efficient genetic transformation.

What is GenomicsWhat is Genomics

??

(Genomics word was coined by Thomas Roderick in 1986.)(Genomics word was coined by Thomas Roderick in 1986.)(Study of structure & function of entire genome of a living organism)(Study of structure & function of entire genome of a living organism)

(Study of the structure Study of the structure of entire genome of an of entire genome of an

organism)organism)

(Study of the function (Study of the function of entire genome of an of entire genome of an

organism)organism)

GENOMICSGENOMICS

Structural GenomicsStructural Genomics Functional GenomicsFunctional Genomics

NEED OF GENOMICS IN RICERice demand: • In each of the next 10 years produce at least 8 million tons rice more

(rough rice) .

Rice supply: • Little change in harvested area(160 million ha)• Yield growth of 1.2-1.5% until 2020 (+50-60 kg/ha/yr)• Yield growth of 1.0-1.2% after 2020

Change how we grow rice: • New seeds to adapt to changing climate• Less tillage, less water, less labour, less pesticides, more efficient

fertilizer use• More resilient, diversified rice-based farming systems

• Is GENOMICS play a role here ?

Rice is the first genome of crop plants sequenced with high precision.Rice is the first genome of crop plants sequenced with high precision.

The rapid advances in genomic research globally, rice research The rapid advances in genomic research globally, rice research

areas summarized in three fronts: areas summarized in three fronts:

construction of technological and resource platforms for high construction of technological and resource platforms for high

throughput gene identification; throughput gene identification;

functional genomic analysis of agronomic traits and biological functional genomic analysis of agronomic traits and biological

processes;processes;

Identification and isolation of functional genes.Identification and isolation of functional genes.

Rice genome is well mapped & well characterized, estimated 400- Rice genome is well mapped & well characterized, estimated 400-

430 Mb430 Mb

Conventional Conventional breeding to molecular breeding to molecular

breeding through breeding through genomic research genomic research

??

Through conventional breeding, selection for crop improvement is carried out on phenotypic character, which is the result of genotypic and environmental effects.

The difficulties of phenotype based selection can be overcome by direct selection for genotype using DNA markers that co segregate with the genes of interest.

Many potential genes that confer resistance have been mapped in economical crops like rice.

9From here… …to here

shifted

In conventional breeding normally options are present of genes can be

identified when expression where comes during adverse condition

By the use of genomic research now we can easily By the use of genomic research now we can easily identify the identify the presence or absence of gene in early stagepresence or absence of gene in early stage

By the use of molecular markers By the use of molecular markers exact location of particular gene exact location of particular gene on on chromosome can easily be identifiedchromosome can easily be identified

Presence of all of the important genes and related markers will be Presence of all of the important genes and related markers will be very much helpful to identified and development of newvery much helpful to identified and development of new cultivars as cultivars as we desire - we desire - Varietal identificationVarietal identification

Insertion and deletions are Insertion and deletions are desirable or undesirable, easily be desirable or undesirable, easily be possible to identify possible to identify with the sequencing of rice.with the sequencing of rice.

Laboratories for genomic research in India Laboratories for genomic research in India

National Research Centre for Plant Biotechnology, IARI, New National Research Centre for Plant Biotechnology, IARI, New Delhi Delhi

International Centre for Genetic Engineering & Biotechnology, International Centre for Genetic Engineering & Biotechnology, New DelhiNew Delhi

Jawaharlal Nehru University , New DelhiJawaharlal Nehru University , New Delhi

National Botanical Research Institute , LucknowNational Botanical Research Institute , Lucknow

Delhi UniversityDelhi University

ICRISAT and DRR ,HyderabadICRISAT and DRR ,Hyderabad

Tools for Genomic ResearchTools for Genomic Research

QTL mapping

DNA sequencing

QTL Mapping QTL Mapping

Character isolationCharacter isolation

Fine-mapping Fine-mapping

Genome scanGenome scanUsing strategies :Using strategies :o Mapping populationMapping populationo PhenotypesPhenotypeso GenotypesGenotypeso Statistical methodologyStatistical methodology

Genome sequencing

Sequence analysis

Gel electrophoresis

DNA fragment elution

Sequencing reaction (Cycle

sequencing)

Sequence alignment(using BLAST- Basic local alignment tool)

Annotation

Sr. No. Rice Sequence Participant Chromosome1. Rice Genome Research Program (RGP), Japan 1 , 6 ,7 , 82. Korea Rice Genome Research Program , Korea 13. CCW (US)

CUG (Clemson University)Cold Spring Harbor University

3 , 10

4. TIGR- US 3 , 105. PGIR-US 106. University of Wisconsin- US 117. National Centre of Gene Research

Chinese Academy of Science – China4

8. Rice Genome Program – University of Delhi 119. Academia Sinica Plant Genomic Center (Taiwan) 510. Genoscope – France 1211. Universidad fedral de Pelotas – Brazil 1212. Kasetsant University – Thailand 913. MG Gill University – Canada 914. John innescenter – UK 2

Institute which sequenced the particular chromosome at RGPInstitute which sequenced the particular chromosome at RGP

Technologies for Implication of Genomics in Rice Crop Improvement

Marker assisted selectionMarker assisted selection

Gene cloningGene cloning

Genetic EngineeringGenetic Engineering

F2

P2

F1

P1 xTolerantSusceptible

Selection based on presence of marker

Marker Assisted Selection (MAS)

Large population consisting of thousands of plants

Genetic Engineering

Gene Cloning

Spikelet morphology of the wild type, eg13, eg11 and F1 progeny from eg13x eg11.(Scale bars, 1 mm)

Positional cloning of EG1 responsible for Jasmonic acid which regulates spikelet development in rice

Application areas of genomic research in riceApplication areas of genomic research in rice

Yield improvement through quicker & efficient discovery and dissection of yield enhancing QTLs and their utilization in marker-assisted breeding/transgenic breeding

Possibility of conversion of rice from a C3 to C4 plant

Understanding the molecular basis of heterosis and cytoplasmic male sterility

Enhanced availability of agronomically important genes for transgenic breeding

Unravelling the pathways/networks associated with abiotic stress tolerance.

Fig: 1 - Number of genes isolated by different methods

Fig: 2 - Functional categories of the isolated genes

Current status of isolated genes in riceCurrent status of isolated genes in rice

Some important genes tagged using molecular markers

Trait Genes Markers Chromosome

reference

Blast

resistance

Pi-1 RZ 536, RG303, NpB 181 11

Pi-2 RG 64.XNpb 294 6

Bacterial

blight resistant

Xa-1 XNpb 235, XNpb 120 4

Xa-21 Y03700 4

Gall midge Gm(2) RG 329, RG476 4 etc.

Gene Trait Country Performance Year

cry1Ab (fromIRRI), cry1Ac

Insectresistance

India Good level of resistance

2002-2005

Xa21 Bacterial blightresistance

China & India(DRR,Hyderabad).

Excellent field performance oftransgenic IR72 in response to BB

2000 &2002-2004

Bar Herbicidetolerance

Bayer, India Good level of tolerance

2005-2007

NHX Salinity tolerance

India Moderate level of tolerance

2005

Gene transformed in IndiaGene transformed in India

Characterization of genes controlling Important traitCharacterization of genes controlling Important trait

Examples of Implication of Genomics Examples of Implication of Genomics in Rice Trait Improvementin Rice Trait Improvement

1. High depth rooting variety development1. High depth rooting variety development

High depth rooting development using Dro1 in IR64

2. Salt Tolerant variety development2. Salt Tolerant variety development

Fig - Schematic diagram of genetic analysis and fine mapping of low glutelin content gene in W3660.

3. Low Glutelin content gene in rice3. Low Glutelin content gene in rice

4. QTL for BLB resistance

• Bacterial Leaf Blight caused by Xanthomonas oryzae pv. Oryzae (Xoo)

• Estimated annual yield loss is 20-60 % (Rice knowledge portal, 2012)

• BLB is wide spread in irrigated and low land rice ecosystem. Growing resistant varieties is the only possible way to tackle the disease.

• More than 30 genes (Xa1, Xa2 …..Xa30) characterized. Genotypes carrying single resistant gene have shown susceptibility at different locations.

• Introgression of multiple R-genes into the genetic background of elite rice varieties with the help of closely linked markers can ensure durable resistance.

5. Bacterial Blight Resistance by MAS5. Bacterial Blight Resistance by MAS

1- Pusa Basmati 1 2- IRBB55

M 1 2 23

950bp

500bp

450bp

xa13 linked marker RG 136

M 1 2 33 M

650bp950bp

Xa21 linked STS Marker pTA 248

IR24 IRBB13 IRBB21 IRBB55 32-6-7-67 PB-1

6. Biofortified Rice Development

7. QTL for submergence tolerance

• A major QTL (Sub1) for submergence tolerance identified and fine

mapped on chromosome 9 in the submergence tolerant cultivar

FR13A

• Sub1A was strongly induced in the tolerant cultivars in response to

submergence, whereas intolerant cultivars had weak or no induction

of the gene

• The grain quality parameters in the Sub1 lines were on par with the

non- introgressed swarna.

•Sub1 variety testing in farmer’s field in India & Bangladesh

•Swarna sub1 is 1st variety released in India & Philippines

Farmer’s field inRangpur (Bangladesh)

Sub1 varieties

Susceptible check

Farmer’s tolerant variety

BR11

BR11-SUB1

Swarna

Swarna sub 1

Farmer’s field,Orissa

GayatriGayatri sub 1

Function of sub1 to keep meristem alive during stress.

Sub1Sub1 and Drought???

The recent integration of advances in molecular biology, transgenic The recent integration of advances in molecular biology, transgenic breeding and molecular marker applications with conventional plant breeding and molecular marker applications with conventional plant breeding practices has created the foundation for molecular plant breeding practices has created the foundation for molecular plant breeding. breeding.

The trinity of DNA marker technology, genetic engineering will The trinity of DNA marker technology, genetic engineering will certainly accelerate rice improvement programmes across the world certainly accelerate rice improvement programmes across the world including India.including India.

Through a judicious application of all these technologies, development Through a judicious application of all these technologies, development of a designer rice plant which is high yielding, using lesser nutrients of a designer rice plant which is high yielding, using lesser nutrients from soil, with tolerance to biotic and abiotic stress and with enhanced from soil, with tolerance to biotic and abiotic stress and with enhanced nutritional quality may be possible in the near future. nutritional quality may be possible in the near future.

There is an urgent need to integrate the recent technology work with There is an urgent need to integrate the recent technology work with mainstream plant breeding to derive maximum benefits from the mainstream plant breeding to derive maximum benefits from the wonderful science of genomic research.wonderful science of genomic research.

CONCLUSION

Some of References

Jiang Y, Cai Z, Xie W, Long T, Yu H, Zhang Q. 2012. Rice functional genomics research: Progress and implications for crop genetic improvement. Biotechnology Advances (30) 1059–1070.

Sasaki T, Wu J, Mizuno H, Antonio BA, and Matsumoto T. 2008. The Rice Genome Sequence as an Indispensable Tool for Crop Improvement. Chapter 1.1, Springer-Verlag Berlin Heidelberg.

Tyagi AK, Mohanty A. 2000. Rice transformation for crop improvement and functional genomics. Plant Science (158) 1–18.

Cai Q, Yuan Z, Chen M, Yin C, Luo Z, Zhao X, Liang W, Hu J & Zhang D. 2014. Jasmonic acid regulates spikelet development in rice. ISSN (online) 2041-1723.

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