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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 Slide 2 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. Blmmel (ILRI), & H. Leung (IRRI); WCA NARS partners: I. Angarawai, I.D.K. Atokple, F. Padi, M.D. Sanogo, O. Sy, & R. Zangr; 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. Bezanon, 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 Slide 3 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 Slide 4 ICRISAT-mandate crops in WCA Sorghum Pearl millet Groundnut Slide 5 Molecular marker development Restriction Fragment Length Polymorphisms (RFLPs) 1980s technology Slow, laborious, expensive & incomplete genome coverage US$2.50 per data point DNA isolation DNA digestion Electrophoretic separation Probe with labels clones Develop image Score polymorphism 300+ polymorphic RFLP loci for pearl millet Genotyping-by-Sequencing Single- Nucleotide Polymorphism Haplotypes Current technology Quicker, cheaper & more complete genome coverage US$40 for 80,000+ data points DNA isolation DNA digestion DNA fragment ligation 95X or 383X pooling Skim sequencing 0.1X to 0.3X Automated SNP allele scoring ca. 275,000 polymorphic GBS-SNP loci for pearl millet 1980s2012 Slide 6 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 3365- entry GCP Sorghum Composite Germplasm Collection Slide 7 Genetic diversity assessment wild bicolor caudatum durra guinea margaritiferum kafir intermediate Slide 8 Molecular marker-based linkage maps & aligned genome sequences Sorghum genome sequence Kresovich et al. (2005) Plant Physiology 138:18981902 Paterson et al. (2009) Nature 457:551556 Physical map of sorghum SSRs Ramu, Deshpande et al. (2010) Molecular Breeding 26:409 418 Millets: genetic & genomic resources Dwivedi et al. (2011) Plant Breeding Reviews 35:247375 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 Slide 9 Physical map of sorghum SSRs Ramu, Deshpande et al. (2010) Molecular Breeding 26: 409418 Slide 10 QTL mapping Conventional bi-parental populations Downy mildew resistance mapping in pearl millet Jones et al. (1995) Theoretical & Applied Genetics 91:448456 Striga hermonthica resistance mapping in sorghum Haussmann et aI. (2004) Theoretical & Applied Genetics 109: 10051016 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 Slide 11 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 84:7988 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 Slide 12 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 locally- preferred varieties from Eritrea: ??? Kenya: Failed as breeding program got too far ahead of marker-data generation Mali: Successful Sudan: Successful advancing towards cultivar release Slide 13 Marker-assisted selection Backcrossing Marker-assisted back-crossing (MABC) Pearl millet 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 51:14441457 Genome-wide selection (GWS) Testing GWS for downy mildew resistance, Striga resistance, & grain yield in pearl millet w/ support from the McKnight Foundation Testing GWS for sorghum in improvement in Mali w/ support from the Generation Challenge Programme Slide 14 Farm-level impact to date Nothing in WCA to date, but early- generation MABC products in farmer- preferred 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 Slide 15 Emerging opportunities GbS-SNPs as a tool for orphan crops White fonio accessions from Mali Aligned crop genome sequences Pearl millet Groundnut Slide 16 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 Slide 17 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) Slide 18 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 Slide 19 Thank you! Thank you! Nagod! Nagod! Fofo! Fofo! Merci de votre attention! Merci de votre attention!