a research project proposal submitted...
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A Research Project Proposal Submitted Under
Accelerated Crop Improvement Programme of the
Department of Biotechnology, Govt. of India.
Title of the project
“Molecular marker-assisted introgression of two major
blast resistance genes and a major QTL for grain yield
under drought stress in rice”
Coordinated by
Agri Biotech Foundation, Hyderabad
Drought Blast
Rice is life
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PROFORMA – I
PROFORMA FOR SUBMISSION OF PROJECT PROPOSALS ON RESEARCH AND
DEVELOPMENT, PROGRAMME SUPPORT
(To be filled by the applicant)
PART I: GENERAL INFORMATION
1. Name of the
Institute/University/Organization
submitting the Project Proposal
Agri Biotech Foundation (ABF), ANGRAU Campus,
Rajendranagar, Hyderabad-500030,
2. State Andhra Pradesh (A.P)
3. Status of the Institute Non Government Organisation (NGOs)
4. Name and designation of the
Executive Authority of the
Institute/University forwarding the
application
Dr. G. Pakki Reddy, Professor, Executive Director
(E.D), Agri Biotech Foundation (ABF), ANGRAU
Campus, Rajendranagar, Hyderabad-500030,
5. Project Title “Molecular marker-assisted introgression of two
major blast resistance genes and a major QTL for
grain yield under drought stress in rice”
6. Category of the Project R & D
7. Specific Area Plant Biotechnology
8. Duration 3 years
9. Total Cost (Rs.) 43 lakhs
10. Is the project Single Institutional
or Multiple-Institutional (S/M)
Multi Institutional
11. If the project is multi-
institutional, please furnish the
following :
Dr. G. Pakki Reddy, Professor, Executive Director
(E.D), Agri Biotech Foundation (ABF), ANGRAU
Campus, Rajendranagar, Hyderabad-500030,
Dr. B.C. Viraktamath,
Project Director,
Directorate of Rice Research (DRR),
Rajendranagar, Hyderabad-500030,
12. Scope of application indicating anticipated product and processes
Two major genes conferring resistance against blast and a major QTL for grain yield under
drought stress in rice will be introgressed into the genetic background of elite rice varieties
grown under rainfed ecosystem of Andhra Pradesh through Marker Assisted Backcross
Breeding (MABB). The improved varieties can be considered for cultivation under areas
affected by blast and drought stresses. Further, the improved breeding lines developed
through the project can also serve as elite donor lines for blast resistance and QTL for grain
yield under drought stress.
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13. Project Summary (Not to exceed one page. Please use separate sheet).
Rice (Oryza sativa L.) is one of the most important staple food crops of the world and is a
primary source of food for more than half of the world’s population. It has been estimated
that demand for rice is expected to be around 125 million tons by 2025 (FAO). Rice
production in India as well as in several other Asian countries must be doubled by 2025 to
meet the requirement of the increasing population. This demand can be met only by
enhancing the production and productivity of rice (Hossain, 1996; Mishra et. al., 2003). In
changing global scenario rice productivity has almost come to its plateau due to erratic
rainfalls, unpredictable weather conditions coupled with increased incidence of biotic and
abiotic stresses. Worldwide drought affects approximately 23 million hectors of rainfed rice
(Serraj et. al., 2011). In the Eastern Indian states (Jharkhand, Orissa, and Chhattisgarh), the
losses are severe (40% of the total production), with an estimated value of US$ 650 million
(Pandey et. al., 2005). This vulnerability to drought is likely to worsen in future due to the
predicted global climate change (Wassmann et. al., 2009a), it is therefore essential to
introduce integrated management strategies at agronomic level by efficient use of available
soil moisture for crop establishment, getting high yield under limited water conditions and
genetic levels by improvement of popular varieties. During water stress conditions or severity
of drought, a major biotic stress- rice blast disease, caused by the filamentous ascomycete
fungus Magnaporthe grisea (anamorph Pyricularia grisea) becomes a serious threat for rice
production and leads to significant yield loss, as high as 70-80 % during an epidemic
(Manandhar et. al., 1992; Khush and Jena 2009). Host plant resistance is very well
documented and exploitation of host plant resistance is considered to be the best option for
management of this disease (Hulbert et. al., 2001). Though, many QTLs were identified for
the yield, the major and stable QTL for yield in the drought stress will be the right candidate
for deployment. Introgression of major genes for blast resistance coupled with stable QTL
for yield under drought stress in the genetic background of elite rice varieties can be
significantly help to tackle the problem of rainfed rice ecosystem. Deployment of such
improved genotypes which can adopt well in limited water conditions possessing blast
resistance can be a viable strategy for mitigating the twin stresses afflicting drought prone
areas. But most of the existing varieties of Andhra Pradesh do not have resistance/tolerance
to cope up with these two challenging stresses. The recent developments in molecular
mapping and marker-assisted selection (MAS) offer a choice of options for targeted
pyramiding of abiotic stress resistance gene/QTL along with major genes of blast resistance
in the genetic background of elite rice varieties. Considering the importance of biotic and
abiotic stresses the present project proposal aims at genetic enhancement of elite rice varieties
viz., Varalu (WGL 14377) and Satya (RNR1446), for high grain yield under drought
tolerance and resistance to rice blast disease through the application of molecular markers.
In this effort, the strategy of marker-assisted backcross breeding will be adopted, wherein
molecular markers closely linked to the target traits will be used for foreground selection,
while microsatellite markers polymorphic between donor lines and recipient varieties will be
used for background selection. Two major genes i.e. Pi1 (Yu et. al., 1991; Fuentes et. al.,
2008) and Pi54 (Madhav et. al., 2005; Sharma et. al., 2005; Ramkumar et. al., 2010)
conferring resistance against blast disease and a major QTL for grain yield i.e. qtl12.1
(Bernier et. al., 2007; Dixit et al., 2012) under drought stress in rice will be introgressed into
the genetic background of elite rice varieties through Marker Assisted Backcross Breeding
with the help of PCR based DNA markers. A simultaneous and stepwise gene transfer
process will be adopted through backcross breeding, which will be continued till BC3
generation and plants possessing the target traits with maximum recurrent parent genome
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introgression (> 95%) will be selfed to generate homozygous lines for evaluation and
advancement. The homozygous stable resistant lines developed through this project will be
evaluated at multiple locations across the country and promising lines will be advanced for
multi-location trials under the All India Coordinated Rice Improvement Project (AICRIP)
and promising entries will be considered for varietal release.
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PART II: PARTICULARS OF INVESTIGATORS
Principal Investigator:
14. Name: Dr. Hari Yadla
Date of Birth: August-30th
, 1978 Sex (M/F): Male
Designation: Assistant Professor/Scientist
Department: Biotechnology
Institute/University: AGRI BIOTECH FOUNDATION (ABF)
Address: Acharya N.G. Ranga Agricultural University Campus, Rajendranagar,
Hyderabad, Andhra Pradesh (A.P), PIN: 500 030.
Telephone: TEL/FAX: 040-24002147/ 9948522760 (Mobile); E-mail:
Number of research projects being handled at present: 2
Co-Investigator
15. Name: Dr. Sheshu Madhav Maganti
Date of Birth: August 24th
, 1972 Sex (M/F): Male
Designation: Senior Scientist
Department: Biotechnology
Institute/University: Directorate of Rice Research (DRR),
Address: Directorate of Rice Research (DRR), ICAR,
Rajendranagar, Hyderabad,
Andhra Pradesh (A.P), PIN: 500030
Telephone: (040) 24015036 Fax: (040) 4015308 E-mail: [email protected]
Number of Research projects being handled at present: 4
Co-Investigator
16. Name:
....................................................................................................…………….............
Date of Birth: ................................................................ Sex (M/F):
......................................
Designation: ...........................................................................................................................
Department:
..........................................................................................................…………..
Institute/University: ...............................................................................................................
Address: ………….................................................................................................................
.........................……………………………………………....... PIN:
.........…......................
Telephone: .................…......... Fax ..............…............. E-mail:………............................
Number of Research projects being handled at present:
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PART III: TECHNICAL DETAILS OF PROJECT
(Under the following heads on separate sheets)
16. Introduction (not to exceed 2 pages or 1000 words)
16.1 Origin of the proposal
Andhra Pradesh is one of the major rice producing state and occupies significant proportion
(~ 30 %) under rainfed ecosystem. In this fragile ecosystem, apart from the drought, blast is
also a severe problem causing huge loss in production and productivity. Two popular
varieties released from ANGRAU i.e. Varalu (WGL 14377) and Satya (RNR 1446) are very
popular in this ecosystem because of their early maturation, preferred grain and cooking
quality along with resistance to biotic stresses like gall midge and moderate level of tolerance
to drought (Varalu), while Satya is tolerant to cold and sheath blight. Varalu (WGL 14377)
and Satya (RNR 1446) also have better nutrient use efficiency, especially uptake of
phosphorus (P). However these varieties suffer from reproductive stage drought stress
coupled with the blast disease, hence genetic improvement of these two varieties will have
advantage of growing them in fragile ecosystem and thereby increasing the yield.
16.2 (a) Rationale of the study supported by cited literature (b) Hypothesis (c) Key
questions.
(a) Rationale of the study:
Blast disease, caused by the filamentous ascomycete fungus Magnaporthe oryzae (anamorph
Pyricularia oryzae), is one of the major threats for rice production and leads to significant
yield loss, as high as 70-80 % during an epidemic (Khush and Jena 2009). The blast disease
is a serious production constraint in the temperate and sub-tropical regions, at high elevation
in tropics and in tropical upland rice in India. Therefore, development of host plant resistance
is considered to be the best option for managing the disease (Hulbert et. al., 2001). Because
of the highly variable nature of the pathogen, resistance conferred by single resistance genes
has broken down and only those varieties possessing multiple resistance genes are effective
over the years at multiple locations. Realizing this, the present project proposal aims at
introgression of two major, dominant blast resistance genes (Pi1 and Pi54) in the genetic
background of elite rice cultivars with the help of molecular markers. It is to be noted that
linked molecular markers are available for these important blast resistance genes (Fuentes et.
al., 2008; Sharma et. al., 2002 and 2005; Ramkumar et. al., 2010).
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Drought tolerance, among the various factors which limit rice production in our country,
abiotic stresses like submergence, salinity, drought, and nutritional disorders are major
constraints to rice production across rainfed rice ecosystems, and they predominantly impact
poor farmers in these areas. Particularly drought is one of the important abiotic stress factors
that limit rice production in upland rice. Worldwide drought affects approximately 23 million
hectors of rainfed rice (Serraj et. al., 2011), in the Eastern Indian states (Jharkhand, Orissa,
and Chhattisgarh), the losses are severe (40% of the total production), with an estimated
value of US$ 650 million (Pandey et. al., 2005). This vulnerability to drought is likely to
worsen in future due to the predicted global climate change (Wassmann et. al., 2009a), it is
therefore essential to introduce integrated management strategies at agronomic level by
efficient use of available soil moisture for crop establishment, getting high yield under
limited water conditions and genetic levels by improvement of popular varieties. A QTL
(qtl12.1) with a large effect on grain yield under stress was originally mapped on
Chromosome 12 at a genetic distance of 10.6 cM region between two SSR markers RM28048
and RM511 (Bernier et. al., 2007). Recently, Dixit et al., (2012) fine mapped the qtl12.1, by
dividing the major QTL into two sub QTLs i.e. qDTY12.1A at a genetic distance of 3.1 cM
region between two SSR markers RM28099 and RM511and qDTY12.1B at a genetic distance
of 0.4 cM region between two SSR markers RM1261 and RM28166. The qtl12.1 also had a
significant effect on a wide range of other traits under severe stress, including biomass yield,
flowering delay, harvest index, plant height, drought-response index, panicle number, and the
number of days to 50% flowering. The Way Rarem derived allele of qtl12.1 was confirmed to
improve grain yield under drought mainly through a slight improvement (7%) in water uptake
under water limited conditions (Bernier et al., 2009)
(b) Hypotheses:
The current high yielding upland rice varieties viz., Varalu and Satya will be improved
through Marker Assisted Breeding by introgression of two major blast resistance genes i.e.
Pi1 and Pi54 and a major QTL for grain yield under drought stress i.e. qtl12.1 coupled with
phenotype based visual selection for good grain quality traits. Therefore the improved lines
developed through the current proposal would replace the existing/original varieties of Varalu
and Satya.
(c) Key Questions:
(i) Whether the major QTL for grain yield under drought tolerance i.e. qtl12.1 will perform
well under the local agro-climatic conditions of Andhra Pradesh
(ii) Whether the QTL introgressed rice varieties will possess better productivity in rainfed
rice ecosystems?
(iii) Whether the newly developed varieties which have the twin characters of grain yield
under drought stress and blast resistance will confer high yield and durable resistance to
blast?
(iv)Whether ‘linkage drag’ associated with QTL introgression/multiple resistance genes be
minimized by following a stringent background selection strategy?
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16.5 Current status of research and development in the subject (both international and
national status)
International Status
Blast: Resistance to blast has been reported to be conferred mainly by the dominant genes.
More than 80 R genes have been reported worldwide. In order to characterize blast resistance
genes used in tropical rice improvements, Mackill, (1985) developed a set of near isogenic
lines (NILs), each containing single major dominant gene. These genes are introgressed from
different donors into indica cultivar, Co-39 which is highly susceptible in the Philippines and
India. Several genes conferring complete and partial resistance, to blast disease have been
located on rice chromosome map (Yu et. al., 1991; Wang et. al., 1994, Pan et. al., 1996).
Blast resistance gene Pi-2(t) and Pi-4(t) have already been tagged with RFLP markers (Yu et.
al., 1991). RFLP mapping of genes conferring complete and partial resistance to blast in
durably resistant rice cultivars were tentatively named Pi-5(t) and Pi-7(t), and mapped on
chromosome 4 and 11, respectively (Wang et al, 1994). A new blast resistance gene Pi-18(t)
has been identified and mapped on long arm of chromosome 11, which conferred resistance
to Korean isolates of M. grisea (Ahn et. al., 2000). They have used already identified RFLP
and microsatellite markers for mapping of this gene in F2 segregating population and they
also concluded that Pi-kh gene was different from Pi-18(t) by the test of allelism (Ahn et. al.,
2000). Chen et. al., (1999) used bulked segregant AFLP analysis and identified two dominant
AFLP markers linked to Pi-44 (t) at 3.3 ±1.5 cM and 11 ± 3.5 cM, respectively. The broad
spectrum blast resistance gene Pi9 from chromosome 6 was cloned and the candidate gene
was identified and found to be encoding nucleotide binding site-leucine rich repeat protein
(Qu et. al., 2006)
Drought tolerance, Drought is one of the important factors that limit rice production in the
most rice-growing areas. Identification of quantitative trait loci (QTL) conferring improved
drought resistance may facilitate breeding progress. Progress in developing high-yielding,
drought-tolerant rice cultivars by conventional breeding has been slow, largely because of
difficulties in precisely defining the target environment, complex interactions of drought
tolerance with environments, and lack of appropriate screening methodology (Cooper et. al.,
1999; Wade et. al., 1999). Considerable work has recently been undertaken to understand the
genetic basis of putative drought-adaptive traits in rice (Chandra Babu et. al., 2003; Courtois
et. al., 2000; Price and Courtois, 1999; Price et. al., 2002a, c; Robin et. al., 2003), but it has
been difficult to identify genetic segments with clear and repeatable effects on yield under
stress. The major challenge facing plant breeders is how to combine the high-yield potential
of modern rice cultivars with robust drought tolerance. It has been suggested that the
development of drought-resistant varieties could be made more efficient by MAS to
introgress alleles of QTL conferring improved drought resistance into the genome of widely
used cultivars through backcrossing.
The identification of genomic regions associated with grain yield and its components under
drought stress will be useful for marker-based approaches to improve grain yield and its
stability for farmers in drought-prone rice environments (Lanceras et. al., 2004). A QTL
(qtl12.1) with a large effect on grain yield under stress was originally mapped on
Chromosome 12 at a genetic distance of 10.6 cM region between two SSR markers RM28048
and RM511 (Bernier et. al., 2007). Recently, Dixit et al., (2012) fine mapped the qtl12.1, by
dividing the major QTL into two sub QTLs i.e. qDTY12.1A at a genetic distance of 3.1 cM
region between two SSR markers RM28099 and RM511and qDTY12.1B at a genetic distance
of 0.4 cM region between two SSR markers RM1261 and RM28166. The qtl12.1 also had a
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significant effect on a wide range of other traits under severe stress, including biomass yield,
flowering delay, harvest index, plant height, drought-response index, panicle number, and the
number of days to 50% flowering. The Way Rarem derived allele of qtl12.1 was confirmed to
improve grain yield under drought mainly through a slight improvement (7%) in water uptake
under water limited conditions (Bernier et al., 2009) Recently, Venuprasad et. al., (2011&
2012) reported two QTLs, i.e. qDTY1.1 and qTDY6.1 for grain yield under upland drought
stress, on chromosome 1 and 6, respectively, however, when compared with qtl12.1,
contribution from these two QTLs for grain yield under drought stress is less.
A marker-assisted backcross (MAB) programme was implemented to improve the root
morphological traits and drought tolerance of ‘Kalinga III’, upland rice variety using
Azucena as the donor parent (Steele et. al., 2006).
National Status
Blast: In 1924, Co4 (Anaikomban) a local race of rice was selected as resistant to blast. Later
TKM1 was recognized as resistant (Padmanabhan, 1979). Further S67 and BJ1 were
identified as resistant to blast disease. Uniform blast nursery (UBN) evaluations of
germplasm accessions have enabled India to develop many blast resistant cultivars
(Padmanabhan 1965). In fact, more than 250 blast resistant high yielding commercial
cultivars have been released in India (DRR, 2001). Yet, genes governing resistance in them
are not characterized. Rice genotypes carrying resistance genes to blast disease were
evaluated in multi-environment tests (METs). Tadukan carrying resistance gene Pi-ta showed
a very high level of durable resistance. A high degree of resistance in A57 carrying three
resistance genes (Pi-1, Pi-2 and Pi-4) was identified across the country, irrespective of
ecosystems. The performance of BL 245 with two resistance genes (Pi-2 and Pi-4) and
C101LAC (Pi-1) was comparable to A57 and the NILs were marginally superior to the
resistant checks (Tadukan, Rasi, Tetep, and IR-64) and the international blast differential
Raminad strain 3 (Muralidharan et. al., 2004).
With high resolution mapping, the Pi-kh gene, (which has been recently renamed as Pi54,
Sharma et. al., 2010) was cloned and characterized to be nucleotide binding site-leucine rich
repeat class of disease resistance genes at NRCPB, New Delhi (Madhav et. al., 2005). Pi54
exhibited resistance to predominant races of the pathogen in India (Sharma et. al., 2002). Pi54
is tagged and mapped on Chr. 11L and an SSR marker RM206 has been reported to be closely
linked to it with a genetic distance of ~ 0.7 cM and is exhibited resistance to predominant races
of the pathogen in India (Sharma et. al., 2002; 2005). Recently, Ramkumar et. al., (2010)
developed a PCR-based functional, co-dominant molecular marker targeting a 144-bp
insertion/deletion (InDel) polymorphism in the exonic region of the gene, named Pi54 MAS.
Earlier studies indicated that through marker-assisted breeding, Pi54 can be introgressed into
hybrid rice parental lines (Hari et. al., 2008; Srinivasarao et. al., 2008; 2009).
Drought Stress,
Quantitative trait loci (QTLs) linked to plant water stress indicators, phenology and
production traits under irrigated and drought stress conditions were mapped by means of a
doubled-haploid (DH) population of 154 rice lines from the cross CT9993-5-10-1-M/
IR62266-42-6-2 (Chandra Babu et. al., 2003). Gorantla et. al., (2006) identified genes
associated with water-stress response in rice by using ESTs generated from a normalized
cDNA library, constructed from drought stressed leaf tissue of an indica cultivar, Nagina 22.
Kanagaraj et. al., (2010) used Bulked Segregant Analysis (BSA) to identify markers linked to
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drought resistance using 23 recombinant inbred (RI) lines of IR20/Nootripathu, two indica
ecotypes with extreme drought response.
16.6 The relevance and expected outcome of the proposed study
The proposed project aims at incorporating two major genes conferring resistance against
blast disease and a major QTL for grain yield under drought stress in rice varieties through
MABB. Marker Assisted foreground selection for above said genes will be carried out using
flanking/directed markers, while marker assisted background selection coupled with
phenotypic selection for agronomic and quality traits will be practiced to hasten the recurrent
parent genome recovery. The project will lead to development of improved versions of
varieties with resistance to blast and increased grain yield under drought stresses. Cultivation
of varieties possessing twin characteristics of high grain yield under drought tolerance and
blast resistance will help farmers reduce the cost of cultivation owing to pesticide use,
improve productivity and will ensure better quality produce to consumers.
Expected outcome
1. Elite breeding lines in the genetic background of Varalu (WGL 14377)/Satya (RNR1446)
possessing high grain yield under drought tolerance and biotic stress resistance (i.e.
drought QTLs + blast resistance) will be developed and evaluated under multiple locations
across the country.
2. Pre-breeding lines in the genetic background of above mentioned rice varieties/cultures
possessing twin characteristics of high grain yield under drought tolerance and blast
resistance will be available for use as donors in gene pyramiding programs.
16.7 Preliminary work done so far
An introgression line of Samba Mahsuri (named SM2545) possessing Pi1 and Pi54 genes in
homozygous condition was developed by Directorate of Rice Research (DRR), which
showed broad spectrum resistance to many isolates of blast pathogen under controlled and at
field conditions of DRR (Srinivas Prasad et. al., 2011). Recently, Pi54 has been introgressed
into hybrid rice parental lines through marker assisted backcross breeding and broad-
spectrum resistance to many isolates of blast pathogen has been reported (Hari et. al., 2008;
Srinivasarao et. al., 2008; 2009).
The Vandana NILs seeds (i.e. IR 84984-83-15-481-B) derived from Vandana × Way Rarem
cross possessing qtl12.1 were evaluated for grain yield and related components by Dr. N. P.
Mandal (Senior Scientist, Plant Breeding) at upland conditions of Central Rainfed Upland
Rice Research Institute CRURRS (CRRI), Hazaribagh-825301, Jharkhand. It was observed
that there is a 30 to 40 % increase in grain yield under drought stress in the plants which
possess qtl12.1 in comparison to the plants which do not possess qtl12.1and this QTL also
had a significant effect on a wide range of other traits under severe stress, including biomass
yield, delay in flowering, harvest index, plant height, drought-response index, panicle
number, and the number of days to 50% flowering. Based on these observations, we
personally communicated Dr. N. P. Mandal, for obtaining seeds of NILs of Vandana
possessing qtl12.1 and he is agreed to share this seed material with ABF.
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17. Specific objectives (should be written in bulleted form, a short paragraph indicating the
methods to be followed for achieving the objective and verifiable indicators of progress
should follow each specific objective)
1. To introgress two major blast resistance genes i.e. Pi1, Pi54 and a major QTL for grain
yield under drought tolerance i.e. qtl12.1 in to the genetic background of upland rice
varieties i.e. Varalu (WGL 14377) and Satya (RNR 1446)
2. To evaluate marker assisted breeding derived lines for blast resistance and grain yield
under drought stress
Recipient genotypes:
Varalu (WGL 14377): This is an early maturing variety with 90-95 days in duration and has
long slender grains with dark brown glumes and good cooking quality traits. It is developed
from a cross between Erramallelu X CR-544-1-2 E and is resistant to gall midge, tolerant to
drought and is suitable for all the three seasons of Andhra Pradesh i.e. Kharif, Rabi and
Yedagaru. It has been released for commercial cultivation in the states of Andhra Pradesh,
Satya (RNR 1446): This variety has long slender grains and is developed from a cross
between Tellahamsa X Rasi. Satya is tolerant to cold, sheath blight. It has been released for
commercial cultivation in the states of Andhra Pradesh,
Donor genotypes and target traits:
Blast resistance: An elite breeding line in the genetic background Samba Mahsuri called
SM2545 with medium slender grain type, possessing Pi1 and Pi54 genes in homozygous
condition will be used as the donor parent for blast resistance.
Drought tolerance: NILs of Vandana possessing qtl12.1, a high yielding, early maturing and
popular indica rice lines suitable for the upland area in India, will be used as a donor parent
for qtl12.1.
18. Work Plan: should not exceed 3-4 pages (the section can be divided according to the
specific aims and under each specific aim, the following should be stated clearly as sub
headings)
18.1 Work plan (methodology/experimental design to accomplish the stated aim)
Detailed work-plan - The present project proposal is aimed for the improvement of the two
rice varieties by introgression of the two major blast resistance genes i.e. Pi1 and Pi54 along
with one major QTL for grain yield under drought stress i.e. qtl12.1 into the genetic
background of Varalu and Satya. The coordinating centre ABF will take care of Varalu,
while the partner institute DRR will take care of Satya.
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Marker-assisted backcross breeding Program at ABF: Introgression of two major BL (Pi1and Pi54) resistance genes and a major QTL for
grain yield under drought tolerance, qtl12.1 into a rice variety, Varalu (WGL 14377)
SM2545 × Varalu NILs of Vandana × Varalu
(Pi1and Pi54) (IR 84984-83-15-481-B, qtl12.1)
F1 × F1 6 months
F1 × Varalu/Satya 12 months
BC1F1 × Varalu/Satya 18 months
BC2F1 × Varalu/Satya 24 months
BC3F1 30 months
BC3F2 36 months
Phenotypic evaluation of BC3F2 lines for blast resistance and grain yield during water
stress conditions or severity of drought under field conditions (Total duration for
completion of project = 3 years)
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Marker-assisted backcross breeding Program at DRR: Introgression of two major BL (Pi1and Pi54) resistance genes and a major QTL for
grain yield under drought tolerance, qtl12.1 into a rice variety, Satya (RNR 1446)
SM2545 × Satya NILs of Vandana × Satya
(Pi1and Pi54) (IR 84984-83-15-481-B, qtl12.1)
F1 × F1 6 months
F1 × Varalu/Satya 12 months
BC1F1 × Varalu/Satya 18 months
BC2F1 × Varalu/Satya 24 months
BC3F1 30 months
BC3F2 36 months
Phenotypic evaluation of BC3F2 lines for blast resistance and grain yield during water
stress conditions or severity of drought under field conditions (Total duration for
completion of project = 3 years)
Breeding-strategy:
Marker-assisted transfer of two major blast resistance genes i.e. Pi1and Pi54 and a major
effect QTL for grain yield under drought tolerance, qtl12.1 into the genetic background of
elite rice varieties:
The strategy of marker-assisted backcross breeding strategy coupled with phenotype-based
selection will be adopted for targeted transfer of Pi1, Pi54 and qtl12.1 into the genetic
background of elite recipient varieties. Marker-assisted foreground selection involving the
co-dominant/functional markers RM224 for Pi1, RM206 and Pi54MAS for Pi54, while
RM511, RM28099, RM1261 and RM28166 for qtl12.1, respectively were used for selection
of target traits. The high-density microsatellite map of rice (IRGSP 2005) provides an
opportunity to practice an effective background selection in favor of recurrent parent genome
in the backcross-breeding program. A set of approximately 150 polymorphic SSR markers
representing 10-12 markers per chromosome will be selected after screening markers at every
5 cM interval from the microsatellite map and used for background selection during
backcrossing. Based on this analysis, a set of SSR markers (~ 60 Nos.), which are
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polymorphic between the donor and recipient genotypes and spread uniformly across the rice
genome will be utilized for background selection. Marker-assisted backcross breeding will be
carried out till BC3 generation and plants possessing Pi1, Pi54 and qtl12.1 gene in
homozygous condition and maximum recurrent parent genome recovery (> 95%) will be
selfed to generated homozygous plants.
List of markers to be used for foreground selection
Trait Genes Molecular
markers
Chr. # References
Blast resistance Pi54 RM206,
Pi54MAS
11 Sharma et. al., 2005
Ramkumar et. al., 2010
Pi1 RM224, RM5926
and RM1233
11 Fuentes et. al., 2008
Drought tolerance qtl12.1 RM511, RM28099,
RM1261 and
RM28166
12 Bernier et. al., 2007
Dixit et al., 2012
Evaluation of the improved lines:
The homozygous stable resistant lines developed through this project will be evaluated first
under controlled conditions at DRR and ABF and later at multiple locations across the
country and promising lines will be advanced for multi-location trials under the All India
Coordinated Rice Improvement Project (AICRIP).
18.2 Connectivity of the participating institutions and investigators (Incase of multi-
institutional projects only)
ABF has validated the molecular markers linked to the qtl12.1 and will be test the NILs of
Vandana (IR 84984-83-15-481-B) possessing qtl12.1 for yield and related components in the
drought prone fields at ANGRAU, Rajendranagar, Hyderabad, Andhra Pradesh and this
information will be shared with partner institute. DRR has already developed markers linked
to the blast resistance genes for Pi1 and Pi54 and being routinely used these two genes in the
breeding programme. ABF will carry out survey of parental polymorphism with SSR markers
for the benefit of the DRR and it will be responsible for a major part of the foreground and
background selection work for DRR. DRR has an excellent blast screening facility and hence
DRR will do the phenotyping of the blast material generated in the project. ABF and DRR
have dedicated drought fields at respective experimental farms. Apart from this, DRR also
have very good grain quality evaluation lab, which will be used in the present project for
selection of the improved lines for grain quality characteristics similar to the recurrent
parents. Over all the connectivity between the partner institutes will be maintained through
regular project performance review meetings, since both the institutes are located very close
to each other.
15
18.3 Alternate strategies (if the proposed experimental design or method does not work
what is the alternate strategy)
Marker assisted selection is a proven technology with high success rate. The only alternate
strategy needs to be adopted is the development of polymorphic markers in case of low
polymorphism between the donor and recipient lines. However with the availability of the
complete genome sequencing, new gene based markers can be designed in case of target
selection and new microsatellite markers for the background selection
19. Timelines: (Please provide quantifiable outputs)
Period of study Achievable targets
6 Months
(Season I)
Phenotypic confirmation of reaction of donor parents
(ABF + DRR)
Validation of markers for foreground selection (ABF +
DRR)
Survey of polymorphism among the parental lines using
SSR markers for deployment in background selection
(ABF)
Development of F1 s by crossing between SM2545
(donor parent possessing blast resistance genes i.e. Pi1
and Pi54) and Varalu/Satya and NILs of Vandana (IR
84984-83-15-481-B, donor parent possessing qtl12.1)
and Varalu/Satya, simultaneously. (ABF + DRR)
ABF
DRR
Parental polymorphism for
BG selection and distribution
of polymorphic markers with
partner institute, DRR Phenotyping
for Drought
tolerance
Coordination and
project review
Phenotyping for
blast resistance
Grain quality
evaluation
Development and
validation of FG
selection markers
Development and
distribution of breeding
materials/populations/
donor lines
16
12 Months
(Season II)
Continuation of parental polymorphism survey (ABF)
Screening of F1s for hybridity using the gene linked SSR
markers RM206 and Pi54MAS for Pi54, RM1233*I and
RM224 for Pi1 and RM511, RM28099, RM1261 and
RM28166 for qtl12.1.(ABF + DRR)
The true F1 plants of both the above mentioned crosses
were intercrossed to combine all the target traits (viz.,
Pi1, Pi54 and qtl12.1) into the genetic background of the
elite rice varieties i.e. Varalu/Satya. (ABF + DRR)
18 Months
(Season III)
The pyramided F1 plants possessing Pi1, Pi54 and qtl
12.1 were confirmed for presence of target traits using
the gene linked molecular markers RM1233*I and
RM224 for Pi1, RM206 and Pi54MAS for Pi54, and
RM511, RM28099, RM1261 and RM28166 for qtl12.1.
(ABF + DRR)
The F1 plants possessing all the target traits were back
crossed with respective recurrent parent(s) to generate
BC1F1 seeds/plants (ABF + DRR)
24 Months
(Season VI)
Foreground and background selection of BC1F1 plants
for selection of ‘best positive’ BC1F1 plant possessing
maximum recurrent parent genome introgression
(ABF + DRR)
backcrossing of the ‘selected’ BC1F1 plants with the
respective recurrent parent(s) to generate BC2F1 plants
(ABF + DRR)
30 Months
(Season V)
Foreground and background selection of BC2F1 plants
for selection of ‘best positive’ BC2F1 plant possessing
maximum recurrent parent genome introgression. (ABF
+ DRR)
backcrossing of the ‘selected’ BC2F1 plants with the
respective recurrent parent(s) to generate BC3F1 plants
(ABF + DRR)
36 Months
(Season VI)
Foreground and background selection of BC3F1 plants
for selection of ‘best positive’ BC3F1 plant possessing
maximum recurrent parent genome introgression.
(ABF + DRR)
Selfing of the ‘best positive’ BC3F1 plant to generate
BC3F2 plants. (ABF + DRR)
Evaluation of homozygous families for target trait(s),
agromorphological traits and for blast resistance and
grain yield during water stress conditions or severity of
drought under field conditions (station trials)
(ABF + DRR)
17
20. Name and adress of 5 experts in the field
S.
No.
Name Designation Address
1
Dr. E. A. Siddiq Honorary
Director
Institute of Biotechnology,
Acharya N.G. Ranga Agricultural
University, Hyderabad – 500 030
Tel:91-40-24018625
Fax : 91-40-24015382
Email:[email protected]
2. Dr. Kuldeep Singh
Molecular
Genetist,
College of Agriculture,
Punjab Agriculture University (PAU),
Ludhiana (Punjab)-141004
Ph:0161-2401960 Ext:270,
M-91-09463504004
Email ID:[email protected]
3 Dr. P.B. Kirti Professor Department of Plant Sciences,
School of Life Sciences,
University of Hyderabad-500046
Email ID: [email protected],
4 Dr. N.P. Mandal
Senior Scientist
(Plant Breeding)
Central Rain Fed Upland Rice
Research Station CRURRS (CRRI),
Hazaribagh-825301, Jharkhand
Phone: (O) 06546-222263,
(R) 06546-224506
Fax: 06546-223697
Mobile: 9430391164
Email ID: [email protected]
5 Dr. H. E. Shashidhar
Professor Department of Plant Biotechnology,
GKVK, University of Agricultural
Sciences Bangalore 560065
Mobile No: 9886319919
E-mail ID: [email protected]
18
PART IV: BUDGET PARTICULARS
Budget (In lakhs)
A. Non-Recurring (e.g. equipments, accessories, etc.): ABF + DRR
S. No Item Year 1 Year 2 Year 3 Total
ABF DRR
- - 6 1 Minor equipments less than 3 lakhs 3 3
Sub-Total (A) = 6 lakhs
B. Recurring
B.1 Manpower: ABF + DRR
S. No. Position
No.
Consolidated
Emolument
Year 1 Year 2 Year 3 Total
1 Junior Research
Fellow (2)
12000 (First
2years) and
14000 for 3rd
year + 30%
HRA
3.744 3.744 4.368 11.856
Sub-Total (B.1) = 11.856 lakhs
B.2 Consumables: ABF + DRR
S. No. Item
Quantity Year 1 Year 2 Year 3 Total
1 Chemicals and
consumables
including
running costs
for existing
equipments
NA 4 lakhs 4 lakhs 4 lakhs 12 lakhs
Sub-Total (B.2) = 12 lakhs
Other items ABF+ DRR:
Other items Consolidated
Emolument
Year 1 Year 2 Year 3 Total
B.3 Travel
1.00 1.00 1.00 3.00
B.4 Contingency
1.50 1.50 1.50 4.50
B.5 Overhead
(A+B)
@ 15% of
budget
5.60
Sub-total of B
(B.1+B.2+B.3+B.4+B.5)
36.96
Grand Total of (A + B) 42.96
Note: Please give justification for each head and sub-head separately mentioned in the above
table.
Financial Year: April - March
In case of multi-institutional project, the budget estimate to be given separately for each institution.
19
PART V: EXISTING FACILITIES
Resources and additional information
1. Laboratory:
a. Manpower
Dr. Hari Yadla (PI), Agricultural Biotechnologist has more than 7 years of experience
in marker assisted selection of rice and extensive experience in hybrid rice breeding.
Elite hybrid rice parental line KMR-3R and its derived hybrid KRH2 has been improved
for bacterial blight resistance and fine grain quality. Elite hybrid rice parental line IR
58025B has been improved for bacterial blight and blast disease through introgression of
Xa21 and Pi-54 resistance genes respectively.
The Co-PI (M. Seshu Madhav) has more than 13 years of experience in marker assisted
selection and he is associated with a projects at DRR for molecular mapping and map
based cloning of blast resistance genes in rice, gene pyramiding of major blast genes
through MAS, Population structure analysis of Maganoporthe, Functional genomics of
quality traits in rice. He also associated with promoter mining for finding tissue and stage
specific promoters and transcriptome analysis of rice.
b. Equipments
The institute (ABF) has a modern Biotechnology Laboratory equipped with all the necessary
sophisticated instruments for carrying out molecular analysis and genetic engineering work.
Besides, there are separate laboratories for each discipline. Most importantly, different
glass/screen houses for screening and evaluation of rice germplasm against all the biotic and
abiotic stresses are available. In addition to an existing contained glass house facility,
recently a new screen house has been built up for evaluation of transgenic rice.
The following are the selected list of instruments/facilities available at the ABF,
biotechnology Laboratory.
S. No Instruments S. No. Instruments
1. Tissue culture facility 10. Microscopes (OLYMPUS all kinds)
2. Molecular Lab 11. Digital Camera
3. PCR Machines (2) 12. Electroporator
4. Gel Doc system 13. Spectrophotometer
5. Refrigerated Centrifuge (1) 14. Incubator shakers
6. Microfuge (2) 15. Digital pen type pH meter
7. Transblot/vacuum blot 16. Growth chambers
8. Gel electrophoresis units (many) 17. Biosafety Glass/polyhouse
9. Deep freez (-20, -80)
2. Other resources such as clinical material, animal house facility, glass house.
Experimental garden, pilot plant facility etc. Available
20
PART VI: DECLARATION/CERTIFICATION
It is certified that
a) the research work proposed in the scheme/project does not in any way duplicate the work
already done or being carried out elsewhere on the subject.
b) the same project proposal has not been submitted to any other agency for financial
support.
c) the emoluments for the manpower proposed are those admissible to persons of
corresponding status employed in the institute/university or as per the Ministry of Science
& Technology guidelines (Annexure-III)
d) necessary provision for the scheme/project will be made in the Institute/University/State
budget in anticipation of the sanction of the scheme/project.
e) if the project involves the utilisation of genetically engineered organisms, we agree to
submit an application through our Institutional Biosafety Committee. We also declare that
while conducting experiments, the Biosafety Guidelines of the Department of
Biotechnology would be followed in toto.
f) if the project involves field trials/experiments/exchange of specimens, etc. we will ensure
that ethical clearances would be taken from concerned ethical Committees/Competent
authorities and the same would be conveyed to the Department of Biotechnology before
implementing the project.
g) it is agreed that any research outcome or intellectual property right(s) on the invention(s)
arising out of the project shall be taken in accordance with the instructions issued with the
approval of the Ministry of Finance, Department of Expenditure, as contained in
Annexure-V.
h) we agree to accept the terms and conditions as enclosed in Annexure-IV. The same is
signed and enclosed.
i) the institute/university agrees that the equipment, other basic facilities and such other
administrative facilities as per terms and conditions of the grant will be extended to
investigator(s) throughout the duration of the project.
j) the Institute assumes to undertake the financial and other management responsibilities of
the project.
Signature of Project Coordinator Signature of Executive Authority
(applicable only for multi-institutional projects) of Institute/University with seal
Date: Date:
Signature of Principal Investigator:
Date:
Signature of Co-Investigator Signature of Co-Investigator
Date: Date:
21
Annexure
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24
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25
PART VII: PROFORMA FOR BIOGRAPHICAL SKETCH OF INVESTIGATORS
Provide the following information for the key personnel in the order listed on PART II.
Follow this format for each person. DO NOT EXCEED THREE PAGES
Name: Dr. Hari Yadla
Designation: Assistant Professor& Scientist
Department/Institute/University: Agri Biotech Foundation (ABF)
Date of Birth: 30/08/1978
Sex (M/F): Male
SC/ST: No
Education (Post-Graduation onwards & Professional Career)
S. No. College/University Degree
Awarded
OGPA/ % of
marks
Year of
Pass
Field of Study
1 ANGRAU,
Rajendra Nagar
Hyderabad, India
M.Sc. (Agri) 81.5 % Jan-2005 Agricultural
Biotechnology
*Title of M.Sc. (Ag.) thesis: “Genetic diversity analysis in the genus Carthamus”
2 Osmania University
Hyderabad, India
Ph. D Degree by
thesis
submission
May-2011 Genetics and
Biotechnology
*Title of PhD thesis: “Improvement of hybrid rice parental lines through marker assisted
selection (MAS)”
A. Position and Honors
Position and Employment (Starting with the most recent employment)
S. No. Institution
Place
Position From (Date) To (date)
1 Agri Biotech Foundation (ABF) Assistant Professor &
Scientist
29.09.2011 Till date
2 Directorate of Rice Research
(DRR)
Research Associate
(RA)
22.09.2007 28.09.2011
2 Directorate of Rice Research
(DRR)
Senior Research
Fellow (SRF)
22.08.2005 21.09.2007
Honors/Awards
Awarded as “Best Poster Award” in a National Symposium entitled “Genomics and
Crop Improvement: Relevance and Reservations” organized by Acharya N. G. Ranga
Agricultural University, Hyderabad during 25-27 February 2010.
Awarded as “Best Poster Award” by Andhra Pradesh Science Congress 2008 entitled
“Emerging trends in Science and technology” organized by AP Akademi of Sciences and
26
Osmania University, held at Osmania University, Hyderabad during 14-16 November
2008.
I was selected as a Senior Research Fellow in an ICAR sponsored network project
entitled on “Gene Pyramiding for resistance to Multiple Biotic stress in Crops” Aug.
2005. Later, based on my performance I have been elevated to the position of Research
Associate since Feb. 2010 in R & D Project entitled “Development of Indica rice lines
with Beta carotene rich endosperm and their evaluation”.
Professional Experience and Training relevant to the Project
Professional Experience
A new TGMS gene tmsdrr has been identified from DRR1S, tagged and fine mapped with
flanking SSR markers RMdrrtms3 and RMdrrtms24 on Chr. 4L and introgressed into the
elite fine-grained high yielding cultivar Samba Mahsuri (BPT5204) through marker-assisted
backcross breeding.
Elite hybrid rice parental line KMR-3R and its derived hybrid KRH2 has been improved for
bacterial blight resistance through introgression of Xa21 gene and fine grain quality (Hari
et. al., 2011).
Elite hybrid rice parental line IR 58025B has been improved for bacterial blight and blast
disease through introgression of Xa21 and Pi54 resistance genes respectively (Hari et. al.,
2008).
Training relevant to the Project
Training details Period and Place of Training
“Molecular Breeding for Rice improvement” Aug 17- 30, 2011
DRR, Hyderabad
“Frontiers of Agricultural Biotechnology” 21st May to 10
th June 2008.
DRR, Hyderabad
“Marker-assisted selection in Rice” July 07-11, 2008. DRR, Hyderabad
B. Publications (Numbers only)
Books: 1
Research Papers: 6 (Foreign), 6 (Indian)
Symposia papers -10
Reports: Nil
General articles: Nil
Patents: Nil
Others (Please specify): Nil
27
Selected peer-reviewed publications (Ten best publications in chronological order)
1. P. Natraj kumar, K. Sujatha, G. S. Laha, K. Srinivasa Rao, B. Mishra, B. C.
Viraktamath, Y. Hari, C. S. Reddy, S. M. Balachandran, T. Ram, M. Sheshu
Madhav, N. Shobha Rani, C. N. Neeraja, G. Ashok Reddy, Hajira Shaik and R.
M. Sundaram (2012) Identification and fine-mapping of Xa33, a novel gene for
resistance to Xanthomonas oryzae pv oryzae. Phytopathology. 102(2): 222-228.
2. Y. Hari, K. Srinivasarao, B.C. Viraktamath, A.S. Hariprasad, G.S. Laha, M. Ilyas
Ahmed, P. Natarajkumar, M.S. Ramesha, C.N. Neeraja, S.M. Balachandran, N.
Shobha Rani, P. Balaji Suresh, K. Sujatha, Manish Pandey, G. Ashok Reddy,
M.S. Madhav and R.M. Sundaram* (2011) Marker-assisted improvement of a
stable restorer line, KMR-3R and its derived hybrid KRH2 for bacterial blight
resistance and grain quality. Plant Breeding 130, 608-616.
3. K. Sujatha, P. Natarajkumar, G.S. Laha, B. Mishra, K. Srinivasa Rao, B.C.
Viraktamath, P.B. Kirti, Y. Hari, S.M. Balachandran, P. Rajendrakumar, T. Ram,
Sk. Hajira, M. Sheshu Madhav, C.N. Neeraja and R.M. Sundaram* (2011).
Inheritance of bacterial blight resistance in the rice cultivar Ajaya and High-
resolution mapping of a major QTL associated with resistance. Genet. Res.,
Camb. 93, 397-408.
4. P. Natarajkumar, K. Sujatha, G. S. Laha, B. C. Viraktamath, B. Mishra, K. Srinivasa
Rao, Y. Hari, S. K. Hajira, K. Pranathi, Ch. Balachiranjeevi, A. Yugander, V. S.
A. K. Sama, S. M. Balachandran, M. Sheshu Madhav, T. Ram, N. Shobha Rani,
C. N. Neeraja, S. K. Mangrauthia and G. Ashok Reddy and R. M. Sundaram*
(2011) Identification, molecular mapping and marker-assisted introgression of
novel bacterial blight resistance genes from wild relatives of Oryza. Ind. J of
Genetics and Plant Breeding. 71: 1-8.
5. R.M. Sundaram, K. Sakthivel, A.S. Hariprasad, M.S. Ramesha, B.C. Viraktamath,
C.N. Neeraja, S.M. Balachandran, N. Shobha Rani, P. Revathi, P. Sandhya, Y.
Hari (2010). Development and validation of a PCR-based functional marker
system for the major wide-compatible gene locus S5 in rice. Molecular Breeding
26:719–727.
6. P. Saidaiah, M.S. Ramesha, R.M. Sundaram and Y. Hari (2010). Molecular Profiling
of Parents of Some Released Rice Hybrids Using SSR Markers. Indian Journal
of Plant Genetic Resources 23: 269-275.
7. K. Sujatha, P. Natarajkumar, G.S. Laha, B.C. Viraktamath, C.S. Reddy, B. Mishra,
S.M. Balachandran, T. Ram, K. Srinivasarao, Y. Hari, P.B. Kirti and R.M.
Sundaram (2010). Molecular mapping of a recessive bacterial blight resistance
gene derived from Oryza rufipogon. Rice Genetics Newsletter 25: 52-53
(Manuscript available online at http://www.shigen.nig.ac.jp/rice/rgn/
vol25/pdf/25_21_9_p_p.pdf).
8. P. Natarajkumar, K. Sujatha, G.S. Laha, B.C. Viraktamath, C.S. Reddy, B. Mishra,
S.M. Balachandran, T. Ram, K. Srinivasarao, Y. Hari and R.M. Sundaram
(2010). Identification of a dominant bacterial blight resistance gene from Oryza
28
nivara and its molecular mapping. Rice Genetics Newsletter 25: 54-56
(Manuscript available online at
http://www.shigen.nig.ac.jp/rice/rgn/vol25/pdf/25_22_13_p_p.pdf).
9. Jaikishen I, Rajendrakumar P, Ramesha MS, Viraktamath BC, Balachandran SM,
Neeraja CN, Sujatha K, Srinivasa Rao K, Natarajkumar P, Hari Y, Ramaprasad
AS and Sundaram RM (2009). Prediction of heterosis for grain yield in rice using
'key' informative EST-SSR markers. Plant Breeding 129: 108-111.
10. P. Rajendrakumar, A.K. Biswal, K. Sakthivel, M.S. Madhav, C.N. Neeraja, S.M.
Balachandran, K. Srinivasarao, P. Natarajkumar, Y. Hari, K. Sujatha and R.M.
Sundaram (2009). Development and validation of class I SSR markers targeting
(GATA)n repeat motifs in rice. Euphytica 169: 263–271.
List maximum of five recent publications relevant to the proposed area of work
1. P. Natraj kumar, K. Sujatha, G. S. Laha, K. Srinivasa Rao, B. Mishra, B. C. Viraktamath,
Y. Hari, C. S. Reddy, S. M. Balachandran, T. Ram, M. Sheshu Madhav, N. Shobha
Rani, C. N. Neeraja, G. Ashok Reddy, Hajira Shaik and R. M. Sundaram (2012)
Identification and fine-mapping of Xa33, a novel gene for resistance to Xanthomonas
oryzae pv oryzae. Phytopathology 102(2), 222- 228
3. Y. Hari, K. Srinivasarao, B.C. Viraktamath, A.S. Hariprasad, G.S. Laha, M. Ilyas
Ahmed, P. Natarajkumar, M.S. Ramesha, C.N. Neeraja, S.M. Balachandran, N.
Shobha Rani, P. Balaji Suresh, K. Sujatha, Manish Pandey, G. Ashok Reddy, M.S.
Madhav and R.M. Sundaram* (2011) Marker-assisted improvement of a stable
restorer line, KMR-3R and its derived hybrid KRH2 for bacterial blight resistance and
grain quality. Plant Breeding 130,608-616
3. K. Sujatha, P. Natarajkumar, G.S. Laha, B. Mishra, K. Srinivasa Rao, B.C. Viraktamath,
P.B. Kirti, Y. Hari, S.M. Balachandran, P. Rajendrakumar, T. Ram, Sk. Hajira, M.
Sheshu Madhav, C.N. Neeraja and R.M. Sundaram* (2011). Inheritance of bacterial
blight resistance in the rice cultivar Ajaya and High-resolution mapping of a major
QTL associated with resistance. Genet. Res., Camb. 93, 397-408
4. R.M. Sundaram, K. Sakthivel, A.S. Hariprasad, M.S. Ramesha, B.C. Viraktamath, C.N.
Neeraja, S.M. Balachandran, N. Shobha Rani, P. Revathi, P. Sandhya, Y. Hari
(2010). Development and validation of a PCR-based functional marker system for the
major wide-compatible gene locus S5 in rice. Molecular Breeding 26:719–727.
5. P. Rajendrakumar, A.K. Biswal, K. Sakthivel, M.S. Madhav, C.N. Neeraja, S.M.
Balachandran, K. Srinivasarao, P. Natarajkumar, Y. Hari, K. Sujatha and R.M.
Sundaram (2009). Development and validation of class I SSR markers targeting
(GATA)n repeat motifs in rice. Euphytica 169: 263–271.
29
C. Research Support Ongoing Research Projects
S. No. Title of Project Funding Agency Amount Date of sanction
and Duration
1 “Improvement of upland rice
for drought tolerance using
Marker Assisted Selection”
Rastriya Krishi
Vikas Yojana
(RKVY),
Government of A.P.
20.00
lakhs
3 years
2 “Biotechnological approach for
controlling Yellow Mosaic
Virus (YMV) in black gram”
Rastriya Krishi
Vikas Yojana
(RKVY),
Government of A.P.
27.86
lakhs
3 years
Completed Research Projects: Nil
Place: Signature of Investigator
Date:
30
BIOGRAPHICAL SKETCH OF CO-INVESTIGATOR
Name : Dr. M. Seshu Madhav
Designation : Senior Scientist (Biotechnology)
Institute : Directorate of Rice Research
Date of Birth : August 24th
,1972
Sex (M/F) : Male
SC/ST : NA
Education (Post-Graduation onwards & Professional Career)
Professional Preparation
Post Doctoral research : Dr. G.L. Wang’s Lab at The Ohio state
University, Columbus, Ohio, USA
PhD (Molecular Biology and Biotechnology): National research centre on plant
Biotechnology (NRCPB) Indian
Agricultural Research Institute (IARI), New
Delhi, India:
M. Sc (Agricultural Biotechnology) : Assam Agricultural University, Jorhat, Assam,
India
B. Sc (Agriculture) A.P, Agricultural University, Hyderabad.
Details of Employment
August 2006 - Till date Sr. Scientist, Biotechnology, Directorate of Rice
research (DRR), Hyderabad, A.P, India.
Feb 2005 -August 2006 Scientist (Sr. Scale), Central Tobacco Research Institute
(CTRI-ICAR) Rajahmundry, A.P
August 2001 -Feb 2005 Scientist, (NRCPB) Indian Agricultural Research
Institute, Delhi, India
April1999- August 2001 Scientist, Central Tobacco Research Institute (CTRI-
ICAR), Rajahmundry, A.P. India
Awards/Honors
Awarded “Jawaharlal Nehru Award for outstanding postgraduate agricultural research
2006” from ICAR, Govt. of India
Awarded “BOYSCAST fellowship (Better opportunities for young scientist in chosen
areas of science and technology)” DST, Govt. of India.
31
Fellow of Association of Biotechnology and pharmacy, India
Patents filled/DNA sequence deposited in Genbank:
Pikh gene and cDNA sequence submitted to Genbank: The annotated genomic DNA and
the cDNA of Pi kh gene was submitted to the genbank. Accession number : AY 914077
Microsatellite clones of tobacco: The 70 genomic clones containing the unique
microsatellite motifs submitted at Genbank. EF 375958 to EF 375992 (34 sequences)
ACC numbers: DQ 865407 to DQ865439 (36 sequence) ACC numbers: DQ 865407 to
DQ865439
Ten alleles including their native promoters of major blast resistance genes Pi Kh, Pita
and three promoter alleles of bacterial leaf blight (BLB) genes Xa21, xa5 and xa13 genes
were cloned from land races and different species of Oryza. These sequences have been
submitted in genbank – NCBI (Acces numbers: GU258499-GU258508, GU269201-GU
269204).
Professional Experience and Training relevant to the Project
March- 2008- Oct- 2009: Post doctoral work on profiling of rice for biotic and abiotic
stress response using deep sequencing technologies at Ohio State University, USA.
Sept 2007- sep 2010: PI of the Project “Promoter mining for identification of novel
regulatory elements of candidate genes in rice for biotic stresses”
July 2008 to till date: Co-PI DBT project “Identification of molecular markers for
important quality characteristics in rice”
September 2009-Present (Co-PI), DBT Project “Identification and Functional analysis of
novel blast resistance genes in rice”. Department of Plant Protection, Directorate of Rice
Research, Hyderabad, India
B. Publications (Numbers only)
Research Papers: 25,
Symposia papers -11,
E-Publications 79 (Genes and other GenBank submissions)
1. G. Ram Kumar, K. Srinivasarao.............M. S. Madhav* (2011).Development and
validation of functional marker targeting an InDel in the major rice blast disease resistance
gene Pi54 (Pikh). Molecualr Breeding (2011) 27:129–135
2. Y. Hari, K. Srinivasarao, B.C. Viraktamath……… M. S. Madhav and R.M. Sundaram*
(2011) Marker-assisted improvement of a stable restorer line, KMR-3R and its derived
hybrid KRH2 for bacterial blight resistance and grain quality. Plant Breeding 130,608-
616 (2011)
32
3. G. Ram Kumar, A.K.P. Sivaranani, Manisk .K. Pandey, K. Sakthivel, N. Shobha Rani, I.
Sudharshan, G.S.V. Prasad, C. N. Neeraja, R. M. SundaramB. C. Viraktamath and M. S.
Madhav * (2010) Development of a PCR-based SNP marker system for effective
selection of kernel length and kernel elongation in rice. Molecular Breeding (2010)
26:735–740
4. G. Ram Kumar, K. Sakthivel, R. M. Sundaram, C. N. Neeraja, S. M. Balachandran, N.
Shobha Rani, B. C. Viraktamath and M.S. Madhav*.(2010). Allele mining in crops:
prospects and potentials. Biotechnology Advances. 28 (2010) 451–461.
5. R. C. Venu, M.Sheshu Madhav,.... Guo-Liang Wang (2010) Deep and Comparative
Transcriptome Analysis of Rice Plants Infested by the Beet Armyworm (Spodoptera
exigua)and Water Weevil (Lissorhoptrus oryzophilus). Rice ( Springer) (2010)3:22–35.
6. G.Ramkumar..........N. Shobha Rani, B.C. Viraktamath and M.S. Madhav* (2010).
Identification of novel alleles of rice blast resistance genes Pikh and Pi ta through allele
mining. International Rice Research Notes. May 2010
7. M. Sheshu Madhav*.... and N. Shobha Rani(2010). Identification and mapping of tightly
linked SSR marker for aroma trait for use in marker assisted selection in rice. Rice
Genetics Newsletter.25:38-40
8. K. Sakthivel, N.Shobha Rani,.......M. Sheshu Madhav….. R.M. Sundaram (2009)
Development of a simple functional marker for fragrance in rice and its validation in
Indian Basmati and non- Basmati fragrant rice varieties.(2009). Mol Breeding 24:185–
190.
9. M. Srinivas Prasad,........ M. Sheshu Madhav (2009). Molecular mapping of rice blast
resistance gene Pi-1(t) in the elite indica variety Samba mahsuri. World .J .Microbiol
Biotechnol.25:1765–1769.
10. M. S. Madhav,T.R. Sharma, ......N.K. Singh (2005). High resolution mapping, cloning
and molecular characterization of Pi kh gene which confers resistance to Magnaporthe
grisea. Molecular Genetics and Genomics .(MGG)Vol.274(6):569 – 578& 671.
List maximum of five recent publications relevant to the proposed area of work
1. G. Ram Kumar, K. Srinivasarao.............M. S. Madhav* (2011).Development and
validation of functional marker targeting an InDel in the major rice blast disease resistance
gene Pi54 (Pikh). Molecualr Breeding (2011) 27:129–135
2. Y. Hari, K. Srinivasarao, B.C. Viraktamath……… M. S. Madhav and R.M. Sundaram*
(2011) Marker-assisted improvement of a stable restorer line, KMR-3R and its derived
hybrid KRH2 for bacterial blight resistance and grain quality. Plant Breeding 130,608-
616
3. G. Ram Kumar, A.K.P. Sivaranani, Manisk .K. Pandey, K. Sakthivel, N. Shobha Rani, I.
Sudharshan, G.S.V. Prasad, C. N. Neeraja, R. M. SundaramB. C. Viraktamath and M. S.
Madhav * (2010) Development of a PCR-based SNP marker system for effective
33
selection of kernel length and kernel elongation in rice. Molecular Breeding (2010)
26:735–740
4. G. Ram Kumar, K. Sakthivel, R. M. Sundaram, C. N. Neeraja, S. M. Balachandran, N.
Shobha Rani, B. C. Viraktamath and M.S. Madhav*.(2010). Allele mining in crops:
prospects and potentials. Biotechnology Advances. 28 (2010) 451–461.
5. M. S. Madhav,T.R. Sharma, ......N.K. Singh (2005). High resolution mapping, cloning and
molecular characterization of Pi kh gene which confers resistance to Magnaporthe grisea.
Molecular Genetics and Genomics .(MGG)Vol.274(6):569 – 578& 671.
D. Research Support
Ongoing Research Projects
S. No. Title of Project Funding
Agency
Amount Date of sanction
and Duration
1 (Co-PI) Identification of molecular
markers for important quality
characteristics in rice”
DBT 35 lakhs July 2008,
3 years
2 (Co-PI) Identification and Functional
analysis of novel blast
resistance genes in rice
DBT 20 lakhs Sep 2009,
3 years
3( PI) “ Identification of molecular
mapping of a novel neck blast
resistance gene(s) from local
land races and introgression
lines of Oryza”
DBT 30 lakhs May 2012
4 (PI) Exploitation of RNAi
technology for management
of yellow stem borer in rice”
DBT 66 lakhs June 2012
Completed Research Projects –
DBT- Rapid grant scheme for young Investigator (RGYI): Completed Sep 2010
Promoter mining for identification of novel regulatory elements of candidate genes in rice for
biotic stresses.
Place: Signature of Investigator
Date: