New genetic tools to improve dryland crop adaptation to abiotic stress and improve crop resistance to pests and diseases C.T. Hash et al. Presented at the symposium: DRYLAND CROP PRODUCTION AND CLIMATE VARIABILITY: 40 YEARS OF RESEARCH PARTNERSHIPS WITH ICRISAT IN WCA during CORAF Science Week, 14-18 May 2012, in Ndjamena, Tchad Co-workers • ICRISAT colleagues: S.P. Deshpande, S. Chandra, S. de Villiers, R.T. Folkertsma, F. Hamidou, M. Kolesnikova-Allen, J. Ndjeunga, T. Nepolean, P. Ramu, O. Riera-Lizarazu, H.F.W. Rattunde, F. Sagnard, S. Senthilvel, T. Shah, S.D. Singh, R.K. Srivastava, Supriya, M. Thudi, V. Vadez, R.K. Varshney, & E. Weltzien; • Other CGIAR colleagues: M. Blümmel (ILRI), & H. Leung (IRRI); • WCA NARS partners: I. Angarawai, I.D.K. Atokple, F. Padi, M.D. Sanogo, O. Sy, & R. Zangré; • American ARI partners: J. Bennetzen, E.S. Buckler, K.M. Devos, S. Kresovich, S.E. Mitchell, A.H. Paterson, & J.P. Wilson; • Australian ARI partners: A. Borrell & D.R. Jordan • British ARI partners: W.A. Breese, C.J. Howarth, E.S. Jones, J. Scholes, D.S. Shaw, J.R. Witcombe, & R.S. Yadav; • French ARI partners: G. Bezançon, C. Billot, M. Deu, J-C. Glaszmann, J-F. Rami, D. This, & Y. Vigouroux; and • German ARI partners: A. Buerkert, H.H. Geiger, B.I.G. Haussmann, & H.K. Parzies Presentation outline • • • • ICRISAT-mandate crops Molecular marker development Genetic diversity assessment Molecular marker-based linkage maps & aligned genome sequences • QTL mapping – Conventional bi-parental populations – Association mapping with inbred germplasm panels • • • • QTL validation Marker-assisted selection Farm-level impact to date Opportunities ICRISAT-mandate crops in WCA Sorghum Groundnut Pearl millet 1980s 2012 Molecular marker development Restriction Fragment Length Genotyping-by-Sequencing SinglePolymorphisms (RFLPs) Nucleotide Polymorphism Haplotypes • 1980s technology • Current technology • Slow, laborious, expensive & • Quicker, cheaper & more incomplete genome coverage complete genome coverage • US$2.50 per data point • US$40 for 80,000+ data points • DNA isolation • DNA isolation • DNA digestion • DNA digestion • Electrophoretic separation • DNA fragment ligation • Probe with labels clones • 95X or 383X pooling • Develop image • Skim sequencing 0.1X to 0.3X • Score polymorphism • Automated SNP allele scoring • 300+ polymorphic RFLP loci • ca. 275,000 polymorphic for pearl millet GBS-SNP loci for pearl millet Genetic diversity assessment Full data set by origin East Asia, India, Middle East, Western Africa, Central Africa, Eastern Africa, Southern Africa, North America, Latin America, & Australia New tools for sorghum 3365entry GCP Sorghum Composite Germplasm Collection Genetic diversity assessment wild bicolor caudatum durra guinea margaritiferum kafir intermediate Molecular marker-based linkage maps & aligned genome sequences Sorghum genome sequence • Kresovich et al. (2005) Plant Physiology 138:1898–1902 • Paterson et al. (2009) Nature 457:551–556 Physical map of sorghum SSRs • Ramu, Deshpande et al. (2010) Molecular Breeding 26:409– 418 Groundnut genome sequence • Peanut-CRISP led consortium w/ ICRISAT as partner Pearl millet genome sequence • ICRISAT led consortium building on rice, sorghum, & Setaria italica aligned genome sequences Millets: genetic & genomic resources • Dwivedi et al. (2011) Plant Breeding Reviews 35:247–375 Physical map of sorghum SSRs Ramu, Deshpande et al. (2010) Molecular Breeding 26: 409–418 QTL mapping Conventional bi-parental populations • Downy mildew resistance mapping in pearl millet – Jones et al. (1995) Theoretical & Applied Genetics 91:448–456 • Striga hermonthica resistance mapping in sorghum – Haussmann et aI. (2004) Theoretical & Applied Genetics 109: 1005–1016 Association mapping w/ germplasm panels • Identification of PhyC as a major gene controlling flowering in pearl millet, with major shifts in allele frequency in Niger between 1976 and 2003 – Vigouroux et al. (2011) PLoS ONE 6(5):e19563 • Candidate-gene approach to mapping flowering genes in West African sorghum – Bhosale et al. (2012) BMC Plant Biology 12:32 QTL validation by MABC & phenotyping Sorghum stay-green • Trait mapped independently in Australia & USA (Purdue & TAMU) • MABC to assess utility of 6 QTLs from donor B35 = BTx642 in different genetic backgrounds – Hash et al. (2003) Field Crops Research 84:79–88 – SARI-led project (Water for Food Challenge Programme), & ICRISAT-led project (Generation Challenge Programme ) • • • • ICSV 111 & S 35 ISIAP Dorado IRAT 204 R 16 Subsequently tested in Ethiopia (release pending for 4 introgression lines), Ghana (again), India, & Sudan QTL validation by MABC & phenotyping Sorghum Striga resistance • QTLs mapped based on phenotyping in Kenya & Mali • Marker-assisted backcrossing to introgress resistance from donor N13 into locallypreferred varieties from – Eritrea: ??? – Kenya: Failed as breeding program got too far ahead of marker-data generation – Mali: Successful – Sudan: Successful advancing towards cultivar release Marker-assisted selection Backcrossing Genome-wide selection (GWS) Marker-assisted back-crossing (MABC) • Pearl millet Testing GWS for downy mildew resistance, Striga resistance, & grain yield in pearl millet w/ support from the McKnight Foundation – Downy mildew resistance – Terminal drought tolerance – Stover nutritional quality (foliar disease resistance) • Sorghum – Shoot fly resistance – Stay-green component of drought tolerance & ruminant nutritional value Backcross nested association mapping (BCNAM) – Jordan et al. (2011) Crop Science 51:1444–1457 Testing GWS for sorghum in improvement in Mali w/ support from the Generation Challenge Programme Farm-level impact to date Nothing in WCA to date, but earlygeneration MABC products in farmerpreferred backgrounds are in pipeline An excellent example from India: • 15 years of ARI/ICRISAT/ NARS collaboration led to release of pearl millet hybrid “HHB 67 Improved” in 2005 • By 2011 this maintenance breeding product was grown on >950,000 ha in Rajasthan & Haryana states, with annual net benefits to farmers estimated at US$20 million, with US$13.5 m to growers there and US$6 m to seed producers in Andhra Pradesh Emerging opportunities GbS-SNPs as a tool for orphan crops Aligned crop genome sequences White fonio accessions from Mali Pearl millet Groundnut Mapping pearl millet Striga resistance • Recently remade cross of wild & inbred parents as mapping population received from US-based partner was mixed up • Produced new plant x plant F1s & advanced these to F3 progenies with DNA sampling of 300 F2 plants – New population segregates for a single recessive gene for male-sterility – Also likely to segregate for root traits, including P-acquisition ability Mapping pearl millet tolerance to low soil P • Assessing performance of 150+ diverse inbreds, & their testcross hybrids, under low and high soil P conditions • Genotyping with SSR, DArT, & GbS-SNP markers • Merge data sets for Association Mapping Similar approach taken in India to identify new QTLs for terminal drought tolerance using a newly developed Pearl Millet inbred Germplasm Association Panel (PMiGAP) Value-chain participatory genome-wide selection • GbS-SNP markers saturate genome enough to permit effective marker-assisted selection for any heritable trait in any species • Need greater than ever for prioritization of breeding targets, use of appropriate experimental designs, generation of high quality phenotype data, and thorough statistical analysis of the resulting data sets • Thank you! • Nagodé! • Fofo! • Merci de votre attention!