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What is happening in peanut genomics in India

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). Groundnut production in India.

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What is happening in peanut genomics in India

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  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. Drought Leaf spot Rust Constraints in production

  4. - Indian Council of Agricultural Research Indian Groundnut Genomics Consortium 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. Mapping water use efficiency QTLs Genetic map construction Collab. D Bertioli, Brazil G He, USA S Knapp, USA Cultivated x Cultivated TAG 24 x ICGV 86031 -RIL

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

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

  11. 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 Generation Challenge Programme(www.generationcp.org)

  12. Director: Jean-Marcel Ribaut (SPL: T van Hintum) (SPL: J-C Glaszmann) (SPL: R K Varshney) (SPL: P Monneveux) (SPL: C de Vicente) GCP Research Structure SP4 DB, Information Network 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 Objectives 1-4 Objective 5 + Activity 2: Generate Genomic Resources Activity 3: Identify Marker Development (Biotic) Activity 4: Identify Marker Development (Abiotic) Activity 5: Improve Germplasm Development Activity 1: Explore Diversity Objective 6 Peanut Cowpea Common bean Chickpea Comparative Genomics Training

  14. 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)

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

  16. 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

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

  18. Contributions and thanks 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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