Breeding Climate-Smart Cowpeas for West Africa
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1 Breeding Climate-Smart Cowpeas for West Africa Phil Roberts University of California Riverside, USA Tim Close, Bao-Lam Huynh, Stefano Lonardi Maria Munoz-Amatriain, Steve Wanamaker UC Riverside Issa Drabo & Joseph Batieno, INERA, Burkina Faso Ousmane Boukar & Christian Fatokun, IITA, Nigeria Ndiaga Cissé, ISRA, Sénégal Rogério Chiulele, E. Mondlane U., Mozambique Francis Kusi, SARI, Ghana Vincent Vadez, ICRISAT, India Jimmy Burridge, Penn. State U.; Tom Sinclair, NCSU PanAfricanWorldCowpea, Mar
2 Cowpea in sub-saharan Africa A Cowpea Forage Vendor Grain vitally important in human diet Kano, Northern Nigeria Forage is highly valued for livestock feed Yacine grain, Senegal 2
3 Partners in semi-arid cowpea zones: INERA, Burkina Faso CSIR-SARI, Ghana IITA-Kano, Nigeria ISRA, Senegal Eduardo Mondlane University, Mozambique 200 mm 600 mm Senegal Burkina Faso Nigeria Ghana 600 mm 200 mm Mozambique
4 Cowpea production zones relative to average annual rainfall in Burkina Faso 300 mm 600 mm 1000 mm
5 Drought events across cowpea growing stages Seedling-stage drought Mid-season drought Terminal drought Planting Seedling Vegetative mid season Flowering Pod filling Harvesting QTLs for early season delayed senescence QTLs for delayed senescence and stay-green
6 Macrophomina phaseolina Devastating under drought Effective resistance available SUS RES Field symptoms in Senegal Ashy stem blight or Charcoal rot
7 Delayed Senescence Phenotyping Early Vegetative stage - Greenhouse Sandbox seedling screen SARI, Ghana Muchero et al. (2008) Crop science 48:
8 Delayed Senescence Phenotyping Early Vegetative stage - Greenhouse SUS Leaf senescence Stem greenness Recovery dry weight TOL
9 Delayed Senescence Phenotyping Vegetative stage field phenotyping Coachella, CA TOL SUS M/SUS
10 Ramping up genotyping capability / /2015 Illumina GoldenGate 1536 SNP assays Fixed Platform LGC (Kbioscience) ~1100 mapped SNPs Customized sets of SNPs Illumina iselect >48,000 SNPs Fixed Platform
11 Drought tolerance QTL identified from both GWAS and Bi-parental mapping Marker Allele Effects: 189 Diverse Genotypes; LD mapping Muchero et al PLoS ONE 8(7):1-10 LD decays between cm ~10x QTL resolution LD mapping 383 diversity panel Nigeria - 339; B Faso - 189; Senegal - 155; USA 200
12 Burkina Faso MARS example Developed F2 from elite parents (Suvita 2, IT97K ). Genotyped 300 F2s with 164 poly SNPs every 2 cm interval. Phenotyped F2:3 families Pobe (low-yielding site) Saria (high-yielding site) Pobe 300 mm Saria 1000 mm
13 QTL detection VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG Yield Yield LOD Score Grain size Yield Grain size Position in the whole genome Favorable alleles from Suvita 2 Favorable alleles from IT97K QTL IciMapping:
14 QTL effects on yield and seed weight Yield-8 (1_0033) GDW-11 (1_0771) Seed weight per plot (g) AA AB BB 100-seed weight (g) AA AB BB 0 10 A: Suvita-2 allele B: IT97K allele
15 Select best families with OptiMAS (IBP-BMS tool) F2:3 Molecular Yield QTLs Kernel-size QTLs Striga family score YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3 Selected Yes Yes Yes Yes Yes Yes No No No No No No (Example list) The Striga QTL is incorporated from prior publication 2002 Genome 45: (Ouédraogo et al.)
16 OptiMAS summary: Frequency of favorable alleles at different selection steps in Burkina Faso MARS (on average and for each QTL) C1 C2 F5 F4 F2 F1 P
17 Yield performance of MARS lines under different rainfall conditions (Saria, Burkina Faso, 2015) Parents MARS positive MARS negative Local checks Drought (Planted on 18 Aug 2015 Rainfall 372 mm) Normal rainfall (Planted on 03 Aug 2015 Rainfall 539 mm)
18 Seed size of MARS lines under different rainfall conditions (Saria, Burkina Faso, 2015) Parents MARS positive MARS negative Local checks Drought (Planted on 18 Aug 2015 Rainfall 372 mm) Normal rainfall (Planted on 03 Aug 2015 Rainfall 539 mm)
19 Illumina BeadChip for Cowpea Position (cm) Illumina BeadChip for Cowpea Reliably assays >48,000 SNPs 37,372 SNPs on current consensus map Available from Illumina since 8/2014 Number of SNPs: 37,372 Number of bins: 3,280 Map size: cm Linkage group
20 350-line 8-parent MAGIC population - founder parents and traits relevant to sub-saharan Africa
21 Cowpea MAGIC population in Coachella Valley, CA in 2015 (47 days after planting) Normal irrigation Restricted irrigation (Drought)
22 Cowpea MAGIC population in Coachella Valley, CA in 2015 (75 days after planting) Restricted irrigation (Drought) Normal irrigation
23 Normal irrigation MAGIC parents in Coachella Valley, CA in 2015 (100 days after planting) IT89KD-288 IT84S-2049 CB27 IT82E-18 Suvita 2 IT00K-1263 IT84S-2246 IT93K Restricted irrigation (Drought)
24 350-line 8-parent MAGIC population field phenotyping under drought S. California, 2015
25 Cowpea variation in N-fixation under drought Should we target these as yet unmapped loci for breeding selection? Sinclair et al., 2015, Crop Science 55:
26 Opportunity to target favorable root traits with QTL mapping and MAS for drought tolerance breeding Photos: J. Burridge
27 Summary Define the target(s) for drought tolerance Associated problems (e.g. diseases under drought) Enhanced genotyping technologies and tools Challenges of phenotyping in TPEs Importance of collaborative partnerships
28 Thank you!
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