Transcript New genetic tools to improve dryland crop adaptation to abiotic
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
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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
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Presentation outline
ICRISAT-mandate crops Molecular marker development Genetic diversity assessment Molecular marker-based linkage maps & aligned genome sequences QTL mapping
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Conventional bi-parental populations
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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
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Molecular marker development
Restriction Fragment Length Polymorphisms (RFLPs) Genotyping-by-Sequencing Single Nucleotide Polymorphism Haplotypes 1980s technology Slow, laborious, expensive & incomplete genome coverage
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Current technology Quicker, cheaper & more complete 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
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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
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 Composite Collection
Genetic diversity assessment
wild bicolor caudatum durra guinea margaritiferum kafir intermediate
Molecular marker-based linkage maps & aligned genome sequences
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Sorghum genome sequence
Kresovich et al. (2005) Plant Physiology 138:1898–1902 Paterson et al. (2009) Nature 457:551–556 •
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 •
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 35:247–375
Physical map of sorghum SSRs
Ramu, Deshpande et al. (2010) Molecular Breeding 26: 409–418
QTL mapping
Conventional bi-parental populations
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Downy mildew resistance mapping in pearl millet
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Jones et al. (1995) Theoretical & Applied Genetics 91:448–456
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Striga hermonthica
resistance mapping in sorghum
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Haussmann et aI. (2004) Theoretical & Applied Genetics 109: 1005–1016 Association mapping w/ germplasm panels
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Identification of PhyC as a major gene controlling flowering in pearl millet, with major shifts in allele frequency in Niger between 1976 and 2003
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Vigouroux et al. (2011) PLoS ONE 6(5):e19563
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Candidate-gene approach to mapping flowering genes in West African sorghum
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Bhosale et al. (2012) BMC Plant Biology 12:32
QTL validation by MABC & phenotyping
Sorghum stay-green
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Trait mapped independently in Australia & USA (Purdue & TAMU) MABC to assess utility of 6 QTLs from donor B35 = BTx642 in different genetic backgrounds
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Hash et al. (2003) Field Crops Research 84:79–88
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SARI-led project (Water for Food Challenge Programme), & ICRISAT-led project (Generation Challenge Programme )
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ICSV 111 & S 35
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ISIAP Dorado
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IRAT 204 R 16 Subsequently tested in Ethiopia (release pending for 4 introgression lines), Ghana (again), India, & Sudan
QTL validation by MABC & phenotyping
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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
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Eritrea: ???
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Kenya: Failed as breeding program got too far ahead of marker-data generation
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Mali: Successful
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Sudan: Successful
advancing towards cultivar release
Marker-assisted selection
Backcrossing
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Marker-assisted back-crossing (MABC) Pearl millet
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Downy mildew resistance Terminal drought tolerance Stover nutritional quality (foliar disease resistance) Sorghum
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Shoot fly resistance Stay-green component of drought tolerance & ruminant nutritional value Backcross nested association mapping (BCNAM)
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Jordan et al. (2011) Crop Science 51:1444–1457 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
Farm-level impact to date
Nothing in WCA to date, but early generation MABC products in farmer preferred backgrounds are in pipeline
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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
White fonio accessions from Mali
Aligned crop genome sequences Pearl millet Groundnut
Mapping pearl millet Striga resistance
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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
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New population segregates for a single recessive gene for male-sterility
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Also likely to segregate for root traits, including P-acquisition ability
Mapping pearl millet tolerance to low soil P
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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
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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
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Thank you!
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Nagodé!
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Fofo!
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