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What is happening in peanut genomics in India

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Presentation on theme: "What is happening in peanut genomics in India"— Presentation transcript:

1 What is happening in peanut genomics in India
Rajeev Varshney Senior Scientist- Applied Genomics, ICRISAT Coordinator, Indian Groundnut Genomics Consortium Leader, Comparative Genomics & Gene Discovery (Generation Challenge Programme)

2 Groundnut production in India
1st most important oilseed crop in India Area: 6.6 million ha Production: 5.9 million t Productivity of groundnut – 0.97 t ha-1 ~ 20% of world production comes from India alone!

3 Constraints in production
Drought Leaf spot Rust

4 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

5 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)

6 What we already have done at ICRISAT…

7 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)

8 Genetic map construction
Collab. D Bertioli, Brazil G He, USA S Knapp, USA Cultivated x Cultivated TAG 24 x ICGV RIL Mapping water use efficiency QTLs

9 Molecular diversity 916 accessions at 21 SSR loci Reference collection
(300 genotypes) fastigiata: 488 hypogaea: 321 wild: 47 Exploring association genetics approach

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

11 Generation Challenge Programme (
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

12 GCP Research Structure DB, Information Network
SP4 DB, Information Network Director: Jean-Marcel Ribaut (SPL: J-C Glaszmann) (SPL: R K Varshney) (SPL: P Monneveux) (SPL: T van Hintum) (SPL: C de Vicente) Phenotyping Phenotyping SP1 Germplasm SP2 Gene Discovery SP3 MAS SP5 Training/Capacity Breeding programmes (Delivery plans) Improved genotypes Improved germplasm in farmers’ fields

13 Tropical Legume I project (GCP) US $ 11 m
Activity 1: Explore Diversity Objective 5 + Activity 2: Generate Genomic Resources Activity 3: Identify Marker Development (Biotic) Activity 4: (Abiotic) Activity 5: Improve Germplasm Objectives 1-4 Objective 6 Peanut Cowpea Common bean Chickpea Comparative Genomics Training

14 Objective 1- Peanut (PI: Dave Hoisington) 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)

15 Objective 5- Cross species (PI: Doug Cook)
David Bertioli Andy Paterson

16 Project partners 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

17 Take home message Community efforts Rapid advances in genomics
Genome infrastructure available Applications to breeding

18 Thank you Contributions and thanks Financial support:
OVERSEAS COLLABORATIONS UC-Davis: Doug Cook, R Varma Catholic Univ: David Bertioli Tuskegee Univ: Guaho He Univ of Georgia: Steve Knapp Genomics: Rajeev Varshney Dave Hoisington Gautami, Ravi, Bryan, SomaRaju Genetic resources: Hari Upadhyaya Ranjana Bhattacherjee Breeding: Shyam Nigam, R Aruna Crop Physiology: Vincent Vadez Statistics & Bioinformatics: Subhash Chandra, Jayashree Collaboartions in India: NRC for Groundnut: T Radhakrishnan UAS Dharwad: MVC Gowda, Khedikar Thank you Financial support: National Fund, Indian Council of Agricultural Research Generation Challenge Programme Department of Biotechnology

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