What is happening in

peanut genomics in India

Rajeev VarshneySenior Scientist- Applied Genomics, ICRISAT

Coordinator, Indian Groundnut Genomics ConsortiumLeader, Comparative Genomics & Gene Discovery

(Generation Challenge Programme)

Groundnut production in India

• 1st most important oilseed crop in IndiaArea: 6.6 million haProduction: 5.9 million tProductivity of groundnut – 0.97 t ha-1

~ 20% of world production comes from India alone!

Constraints in production

Drought

Leaf spot

Rust

Indian Groundnut Genomics Consortium

- Indian Council of Agricultural Research

Three main partners:

ICRISAT, Patancheru, A.P. (Intern. Crops Res. Inst. Semi-Arid Tropics)

NRCG, Junagadh, Gujarat (National Research Centre for Groundnut)

UAS, Dharwad, Karnataka (University of Agricultural Sciences)

Team of multidisciplinary scientists

Activities• Generation of microsatellite-enriched libraries and

identification of ~500 microsatellite or simple sequence repeat (SSR) loci

• Generation of groundnut unigene-derived SNP markers and development of cost effective CAPS assay

• Construction of integrated genetic maps with SSR, SNP and DArT markers

• Phenotyping of mapping populations at three locations (ICRISAT, NRCG, UASD) over 3 years

• Identification of genes/QTLs associated with resistance to foliar diseases (rust and late leaf spot) and tolerance to drought (TE, SCMR and SLA)

What we already have done at ICRISAT…

SSR marker development In silico approach after mining sequence data

- Aeschynomenoid/ Dalbergoid and Genistoid clades of the Leguminoae (15 genera)

- 6 genera Adesmia, Amorpha, Dalbergia, Chaetocalyx Lupinus and Stylosanthes: 411 seqs contained SSRs. - Primer pairs for 109 unique SSRs

- 79 functional in one of six genera - 51 primer pairs functional in peanut

BAC-end sequence derived SSRs (Doug Cook)

Genetic map construction

GM635a0.0

GM635b5.9

seq18G09_5B10.7seq13A0711.6GM66914.5

seq17E0119.0

TC3G01a48.4TC3G01c50.1

Ah1

GM6300.0seq10D043.3RN6F056.2GM6337.6PM1799.4TC6E0114.5

GM66742.6

Ah2

GM6260.0

seq16C0615.5

seq13E0930.3

Ah3

TC3G01b0.0

XIP21918.0XIP60624.3XIP41926.5XIP12328.1PM72129.2GM66029.8GM67931.5XIP17733.8XIP40635.9TC9F10_8A37.4TC6H03_6B39.2PM733a40.9

Ah4

TC7C060.0

XIP24511.0

GM62316.4TC1A02_7B18.9XIP68922.6

TC1A0128.4

PM37734.8

seq9H08a38.6

XIP171A46.1

Ah5

RI1F06_2A0.0

seq18E078.6

seq1B0917.1PM49918.9

PM7325.3

AC2C0534.6

seq2G0450.8

TC9F0462.0

Ah6

seq18G010.0

seq19D019.8

Ah7

GM6980.0

seq8H0122.5

Ah8

seq7G020.0

gi1170_9A18.6Lec1_9A20.7PM43622.7GM69426.8seq14H0628.8

TC5A0634.5

Ah9.1

seq2B090.0

GM67214.6TC2D0616.2

Ah193_1A23.6

seq13A1032.9

Ah9.2

XIP2870.0

seq9G0513.9

seq19D0627.1

GM723b37.3

seq19H0343.7

PM18361.8

PM41875.6

Ah10

TC11B040.0

GM64723.6

TC7H11_2A42.1

GM69260.8

Ah11

TC4D090.0

XIP52410.3

seq19A0522.5XIP16524.6

Ah12

PM4270.0

PM3757.7GM62910.8GM73613.2

seq18C0523.9XIP108B26.1

XIP13661.1

Ah14

GM6980.0

seq8H0122.5

Ah8

seq7G020.0

gi1170_9A18.6Lec1_9A20.7PM43622.7GM69426.8seq14H0628.8

TC5A0634.5

Ah9.1

seq2B090.0

GM67214.6TC2D0616.2

Ah193_1A23.6

seq13A1032.9

Ah9.2

XIP2870.0

seq9G0513.9

seq19D0627.1

GM723b37.3

seq19H0343.7

PM18361.8

PM41875.6

Ah10

TC11B040.0

GM64723.6

TC7H11_2A42.1

GM69260.8

Ah11

TC4D090.0

XIP52410.3

seq19A0522.5XIP16524.6

Ah12

PM4270.0

PM3757.7GM62910.8GM73613.2

seq18C0523.9XIP108B26.1

XIP13661.1

Ah14

XIP1050.0

XIP108A6.7

Ah15

TC4G020.0

GM61836.7

Gi492651.9

GM74562.9

seq18A0567.5

seq19G0783.0

Ah16

GM6240.0

seq19B125.4TC9H099.0

seq15C1020.1

Ah17

seq11G030.0TC4F12_2A3.8

Ah18

seq19D09_1B0.0

TC7E0435.4

Ah19

GM6410.0

seq16G0847.3

Ah20

Cultivated x Cultivated

TAG 24 x ICGV 86031 -RIL

Mapping water use efficiency QTLs

Collab.D Bertioli, BrazilG He, USAS Knapp, USA

Molecular diversity

fastigiata: 488hypogaea: 321wild: 47

916 accessions at 21 SSR loci Reference collection(300 genotypes)

Exploring association genetics approach

What we plan to do at ICRISAT (under Troplical Legume Genomics project)…

Generation Challenge Programme(www.generationcp.org)

• Launched in August 2003• 10-year framework (2004–2008; 2009–2013)• About US$16M annual budget

– 75% Research– 15% Training and capacity building– 10% Management cost

• Major donors– European Community– DFID– The Bill & Melinda Gates Foundation– World Bank – Switzerland

• Target areas: Marginal drought-prone environments– Africa (SSA)– South and South East Asia – Latin America

• Mandate crops (CGIAR) – 22 crops• A CGIAR Challenge Programme hosted at CIMMYT, Mexico

SP4DB, Information Network

SP5Training/Capacity

SP1Germplasm

SP2Gene Discovery

SP3MAS

Improved germplasm in farmers’ fields

Phenotyping Phenotyping

GCP Research Structure

Breeding programmes

Improved genotypes

(Delivery plans)

Director:

Jean-Marcel Ribaut

(SPL: J-C Glaszmann) (SPL: R K Varshney) (SPL: P Monneveux)

(SPL: T van Hintum)

(SPL: C de Vicente)

Activity 1:Explore

Diversity

Objective 5 + Activity 2:

GenerateGenomic Resources

Activity 3:Identify Marker

Development(Biotic)

Activity 4:Identify Marker

Development(Abiotic)

Activity 5:Improve

Germplasm Development

Ob

ject

ives

1-4

Objective 6

Tropical Legume I project (GCP) US $ 11 m

PeanutCowpea

Common beanChickpea

Comparative GenomicsTraining

Project Activities• Develop germplasm for genetic studies and modern

breeding– Bonny Ntare (ICRISAT, Mali)

• Generate genomic resources for genetic studies and modern breeding– Andy Paterson (University of Georgia, USA)

• Identify molecular markers and genes for biotic stress resistance– David Bertioli (Catholic University, Brazil)

• Identify molecular markers and genes for drought tolerance– Vincent Vadez (ICRISAT, India)

• Improve locally adapted germplasm for target traits through modern breeding– Emmanuel Monyo (ICRISAT, Malawi)

Objective 1- Peanut(PI: Dave Hoisington)

Objective 5: Develop cross species resources for comparative genomics in tropical crop legumes

Activity 1:

Milestones:

3. Associate genetic markers to bacterial artificial chromosome clones in each species

Activity 2:

Milestones:5. Mapping of orthologous genetic markers in diploid Arachis AA population6. Identification of ultra-long SSRs in tetraploid Arachis7. Genetic mapping of ultra-long SSRs in tetraploid Arachis

Activity 3:

Milestones:

Comparative Marker Development

4. Diploid Arachis AA bacterial artificial chromosome clone end sequencing and SSR discovery

1. Development of molecular marker database and web interface.

8. DNA sequencing and divergence estimates for network of orthologous bacterial artificial chromosome clones

2. Development of 500 orthologous gene markers.

Analysis of the Arachis-species Complex

Estimating Genome Divergence at Orthologous Loci

Objective 5- Cross species(PI: Doug Cook)

Doug Cook

David Bertioli

Andy Paterson

• Catholic University of Brasilia, Brazil• Chitedze Research Station, Department of

Research and Development, Ministry of Agriculture, Malawi

• EMBRAPA, Brazil• ICRISAT, India/Malawi/Mali• Insitut National de Recherche Agronomique du

Niger (INRAN), Niger • Institut Sénégalais de Recherche Agricole

(ISRA), Senegal• Naliendele Research Station, Department of

Research and Development, Ministry of Agriculture, Tanzania

• University of Georgia, USA

Project partners

Community efforts Rapid advances in genomics Genome infrastructure available Applications to breeding

Take home message

Genomics:Rajeev Varshney Dave HoisingtonGautami, Ravi, Bryan, SomaRaju

Genetic resources:Hari UpadhyayaRanjana Bhattacherjee

Breeding:Shyam Nigam, R Aruna

Crop Physiology:Vincent Vadez

Statistics & Bioinformatics:Subhash Chandra, Jayashree

Collaboartions in India:NRC for Groundnut: T RadhakrishnanUAS Dharwad: MVC Gowda, Khedikar

OVERSEAS COLLABORATIONSUC-Davis: Doug Cook, R Varma

Catholic Univ: David Bertioli

Tuskegee Univ: Guaho He

Univ of Georgia: Steve Knapp

Contributions and thanks

GenerationChallengeProgramme

National Fund,Indian Council of Agricultural Research

Department of Biotechnology

Financial support:

Thank

you