Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India
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Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India presentation by "Douglas Cook, University of California Davis, Davis, United States of America"
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Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India
- 1. http://chickpealab.ucdavis.edu United States, Ethiopia, India, Pakistan, Turkey, Australia, Canada, Morocco Domestication Modern breeding Regionaldiversification WildRelatives Abiotic stress, Biotic stress, Nitrogen fixation, Nutrition, Agronomic traits Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India
- 2. Chickpea is the world’s 2nd most important grain legume and critical to food security in much of the developing world •Stagnant yields •Susceptible to pathogens, pests and abiotic stress • Drought • Heat • Pests and Disease • Nitrogen fixation • Nutrition • Soil adaptation • Domestication 11
- 3. Domestication Modern breeding Regionaldiversification WildRelatives 6.7M variants 0.172 M variants Wild species Modern elite varieties ~95% loss of variation 26 representative wilds 29 modern elite varieties Crop improvement requires a source of variation
- 4. Nitrogen fixation and domestication Migrating adaptive alleles from wild to cultivated Drought tolerance Sponsor and Partner Institutions
- 5. Our target countries • Regularly impacted by climatic extremes Ethiopia • 40% of Africa’s chickpea production • Historical focus of domestication India • Major consumer and producer of chickpea. • Among the lowest yielding countries.
- 6. Terminal drought: year in, year out, most serious constraint.
- 7. Plant a er the rains. Produce crop on residual soil moisture. Exposes crop to drought.
- 8. Ascochyta blight is a climate-driven disease, and o en the limi ng factor in chickpea produc on Fusarium wilt Pod borer
- 9. Plant a er the rains Climate-driven shi s in the microbiome drive cul va on prac ces Early plan ng increases risk of: 1. Foliar Ascochyta blight 2. Soil seedling diseases Both diseases are driven by high moisture. Cul va on too late in season = increased risk of: 1. Drought and Heat 2. Fusarium infec on 3. Pod borer Abiotic and biotic stress drive cultivation practices
- 10. Accessing, characterizing and utilizing genetic variation Breeding needs variation
- 11. Wild systems: Starting in south-eastern Turkey Turkey Syria Iraq Iran C.arietinum C.reticulatum C.echinospermum Using all 19 variables for Bioclim on DIVA-GIS
- 13. Time-series analyses: how effects of G changed over ~100 years of climate / environment change 0 500 1000 1500 2000 2500 3000 1911 1914 1917 1920 1923 1926 1929 1932 1935 1938 1941 1944 1947 1950 1953 1956 1959 1962 1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001 2004 #ofAccessions # Date of acquisition Percentofcollection Ethiopia*(87) India (261) Turkey (75) 39
- 14. We explored chickpea’s center of origin over 56 days in 2013 and 100 days in 2014/15 at ~50 sites Egil 1 2 3 4 5 6 C.arietinum C.reticulatum C.echinospermum In the wild: 1002 Km
- 15. How do you survey variation for climate resilience? Altitude: 600m – 2,000m Rainfall gradients Seasonality Temperature Humidity Soil types Microbial communities Co-occurring species
- 16. Understand environmental heterogeneity soils co-occurring species abiotic factors spatial and temporal variation
- 17. DNA from thousands GBS and WGS population genomics in situ association genetics C. reticulatum C. echinospermum Egil 1 2 3 4 5 6 Predominant focus of historical germplasm 1,100 accessions 2013 ~1,000 accessions 2014/2015 Cicer reticulatumCicer echinospermum Karabace S2DR Gunas Cermic Destek Guven Derici Kesantas Oyali Sarikaya Kayatape Kalkan Egil Besevler Savur Bari2 Bari3 Bari1 Cudi1 Cudi2 Sirnak Ortanca RKesen RCNTRL REgill RKalka RBesev RSavur RKayat Rnpgs RDerei RSarik RBari3 RBari2 RBari1 ROyali RCudiA RCudiB RSirna EDeste EGunas ECermi Enpgs ERdsde ES2Drd EKarab EOrtan EGuven
- 18. How will we make the wild alleles useful for breeding?
- 19. Evaluation Strategies In situ association genetics for candidate gene nomination Association genetics with phenology-normalized NAMs Advanced backcross introgression lines Breeding Ecology and population genomics Phenotyping Trait discovery Genomics-driven Introgression
- 20. Domestication: 10-12,000 years ago Secondary diversification: ~6,000 years ago Secondary diversification: ~3-4,000 years ago 6.7M variants 0.172 M variants •3 High quality reference genomes: BioNano OM, PacBio, Illumina, dense SNP maps •26 deep representative wilds (30X) •250 moderate wilds (10X) •750 shallow wilds with imputation •29 cultivated from international project Developing genomic platforms Wild species Modern elite varieties ~95% loss of variation
- 21. Cicer reticulatumCicer echinospermum Karabace S2DR Gunas Cermic Destek Guven Derici Kesantas Oyali Sarikaya Kayatape Kalkan Egil Besevler Savur Bari2 Bari3 Bari1 Cudi1 Cudi2 Sirnak RKesen RCNTRL REgill RKalka RBesev RSavur RKayat Rnpgs RDerei RSarik RBari3 RBari2 RBari1 ROyali RCudiA RCudiB RSirna EDeste EGunas ECermi Enpgs ERdsde ES2Drd EKarab EOrtan EGuven Ortanca 270 accessions in the multi- lateral system. Hundreds of additional accessions in partner institutions in Turkey >26 wild accessions x 5 elite cultivars in pre-breeding pipeline (NAMs and ABIs). ~5,000 Segregating F3 Developing genetic resources: pre-breeding, trait and gene discovery
- 22. Microbes impart functional properties (i.e., “health”) to their plant hosts. … but we lack a solid understanding of these phenomena Micronutrient uptake Drought Tolerance Phosphate solubilization Disease Tolerance Nitrogen Fixation Micronutrient uptake Drought Tolerance Phosphate solubilization Disease Tolerance Nitrogen Fixation ? ? ? ? ? ? ? ? ? ? ? ?
- 23. Systematically collect and characterize chickpea’s microbiome 0.2 M.gobiense Mesorhizobiumsp. M.plurifarium M.chacoense USDA-4473 Ensiferfredii USDA-4267 M.cicerisv.biserrulae 2P3S1-b Azorhizobiumcaulinodans Bradyrhizobiumjaponicum M.amorphae USDA-4332 M.loti CV-18-Elvas M.tianshanense cw-197 M.temperatum M.septentrionale USDA-10001 M.metallidurans M.albiziae E.meliloti USDA-4213 24P3S1 M.tarimense E.medicae Rhizobiumetli USDA-4779 cw-159 Ethiopia India Turkey (Cicer reticulatum) USA Canada Australia Turkey (Cicer echinospermum) 0 5 10 15 20 25 30 400060008000100001200014000 Group 2 Pangenome Gene Accumulation Plot Genomes Genes Global collection of Nitrogen-fixing Mesorhizobium X X X X X1 2 4 3 5 6 7 Chickpea’s microbiome
- 24. Pathogens Symbionts Commensals Host Environment Genetic resiliency to extreme and variable climates requires a holistic approach
- 25. Abiotic stress: Drought, heat, cold Biotic stress: Fusarium, Pod borer, (Ascochyta) Nitrogen: Symbiosis and nitrogen “metabolism”. Nutrition: Inorganic and organic composition. Agronomic traits: Architecture, flowering time. Phenotyping and trait targets
- 26. UC Davis Doug Cook Varma Penmetsa Noelia Carrasquilla Alex Greenspan Betsy Alford Susan Moenga Lisa Vance Peter Chang Bullo Mamo Brendan Riely Gul Abbas Dagnachew Bekele Zahra Samiezade-Yazd Lei Feng Ping Song Shraddha Suman Florida International Univ Eric von Wettberg ICRISAT Vincent Vadez Hari Sharma Assam Agric Univ Bidyut Sarmah Punjab Agric Univ Sarvjeet Singh Harran University Adbullah Kahraman Dicle University Bekir Bukun Fatma Basdemin AARI Ali Peksuslu Lerzan Aykas Abdullah Inan Turkish Ministry of Ag Abdulkadir Aydogan Husseyin Ozcelik Mahmut Gayberi CSIRO WA Jens Berger John Thompson Wendy Vance Judith Lichtenzveig Graham O’Hara Banaras Hindu University Birinchi Sarma UAS-Dharwad Bhuvaneshwara Patil EIAR Asnake Fikre Lijalem Balcha Kassaye Dinegde Zehara Damtew Dagnachew Bekele Tsegaye Getahun Gashaw Bedada Sultan Yimer Addis Aababa Univ Kassahun Tesfaye Fassil Assefa Masresha Fetene USC Sergey Nuzhdin Peter Chang Vasantika Singh Matilde Cordeiro Min-Gyoung Shin ICARDA Michel Ghanem Sripada Udupa Ege University Bhattin Tanyolac U Saskatchewan Bunyamin Taran Research Partners and Institutions