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40 Jeff Ehlers Tli Objective2 Phase Ii Work Plan


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40 Jeff Ehlers Tli Objective2 Phase Ii Work Plan

  1. 1. TL-I Objective 2 Phase 2 Draft Workplan – Nov. 20, 2009 “Improving Cowpea Productivity for Marginal Environments in SSA” UC Riverside and IITA (Jeff Ehlers, Phil Roberts, Tim Close, Ousmane Boukar) N. Cisse - ISRA, Senegal I. Drabo - INERA, Burkina Faso R. Chiulele - Eduardo Mondlane University, Mozambique
  2. 2. Partners located across semi-arid “cowpea zone”: IITA – Kano, Nigeria INERA, Saria, Burkina Faso ISRA, CNRA-Bambey, Senegal Eduardo Mondlane Univ., Maputo, Mozambique 200mm Senegal Burkina Faso Nigeria 800mm UCR Field Station mimics Africa Mozambique
  3. 3. Rationale   Cowpea is a key component of cropping systems, food security in SSA   Cowpea productivity impacted by: • Drought, heat; Macrophomena, bacterial blight, flower thrips, aphids, Striga,nematodes   Solution – Cowpea varieties that resist these stresses   “Modern Breeding” speeds delivery •  Apply the outputs of current TL-1 in new breeding strategies (MARS, MABC) •  Transfer Phase I outputs to TL-2   High-throughput SNP genotyping   Markers for drought and biotic stress resistance   Agarose-gel based markers from SNPs
  4. 4. TL-1 Linkages to 8 African partners TL-1 TL-2 UCR/IITA IITA CRSP CRSP CRSP TL-1,2 TL-2 TL-2 TL-2 TL-2 Senegal Angola Burkina Moz. Mali Tanz. Niger Nigeria EMU, IIAM IITA
  5. 5. Phase 2 will build on current outputs of TL-1 & TL-2   Drought tolerant germplasm and drought QTL identified   Key QTL for resistance to flower thrips, Macrophomina, root-knot nematode   High-throughput SNP genotyping •  Essential tool for MARS, MABC •  Select single-plex SNPs– custom assays   High density SNP consensus map (Muchero et al., PNAS, 2009) 680cM; 11 LG; 1 marker/0.7cM 5 
  6. 6. Activity Phase I Outcomes, deliverables to TL-2 and Phase 2 Workplan & Outcomes Tools Output TL-1 and TL-2 TL-1 and TL-2 Genomic Phenotyping, Marker Germplasm Population Resources Development Outcome Screening development Transfer. cDNA, EST sequencing Outcome >1,500 Accessions 1,200 RIL Crosses made and phenotyped drought tolerance Phenotyped- Drought advanced High-throughput SNP tolerance & biotic Phase I genotyping platform resistance 1,200 RIL genotyped 1536 SNPs Agarose gel markers 640 access genotyped 1536 SNPs (50 TL-2 FPV, Elites) SNP QTLs Drought, Striga, Macro, Sources of drought Consensus map Nematodes, Thrips Elite x Elite tolerance w/1000 SNPs Populations Genotyping, MARS ; MABC Training Data Management TL-1 MAGIC MARS Tools population Phase II QTL Analysis High-throughput SNP genotyping platform TL- 2 IITA/NARS 8 elite x elite , 2 cycles MAS & MABC; MARS; 8 MABC sets of lines Test, release Release DT varieties cultivars, Parents 3 PhDs trained Test - MARS efficiency, 7 NARS breeders practicality 24 advanced lines w/ trained superior 2014 Identification of genes for performance under important traits drought; 8 MABC lines then
  7. 7. Activity 1: Develop MAGIC population SNP genotypes for the eight prospec3ve parents for linkage  group 1 are shown below as an example.
  8. 8. Activity 2: Develop genomic resources in support of marker-assisted breeding •  Customized sets of markers for MARS ; genotype data production in support of MARS breeding •  Genotyping data analysis to optimize MARS (breeding values, selection indices) •  Genetic analysis for QTL discovery in MARS populations
  9. 9. Activity 3: Employ MARS and MABC to develop improved breeding lines •  2 populations per partner, 300 lines/population •  Conduct MARS cycles 1 and 2 in elite x elite crosses •  Selection and performance testing of advanced lines 2010 2011 2012 2013 2014 May May May May Aug Sep Nov Dec Aug Sep Nov Dec Aug Sep Nov Dec Aug Sep Nov Dec Feb Mar Feb Mar Feb Mar Feb Mar Jun Jan Jun Jan Jun Jan Jun Jan Oct Apr Oct Apr Oct Apr Oct Apr Jul Jul Jul Jul Phenotyping of parents (Phase 1 Output) Sow Parents, Cross, Harvest F1(greenhouse) Sowing of 6 F1; Harvest F2 Sowing of 6 F2; Harvest 6 F3 (300 each) Sow F3; Genotype F3; Harvest F4 seed Phenotype F4 Families; select 10% Genotype 5/family, recombine selected 4 F5 (Crosses) Sow Recombined (F1), Harvest 4 F2 Genotype 400 F2, select 100; harvest F3 selected Phenotype 100 F3, Select 10% -, Harvest F4 seed Genotype 5/family, recombine selected F4, also advance selects to F5-tests Genotype, advance F5 to F6 Performance evaluation to determine progress 10x 30x 10x 10x 10x 10x 10x 10x Genotyping Needs/popln 92 5 300 300 5 5 2 400 5 5 5 5 100 300 No. of Populations 2 2 6 2 6 2 2 6 6 2 6 6 6 6 Total=10,727 samples to be 180 240 180 genotyped 184 100 0 600 900 100 40 0 300 100 300 300 600 0 **Yellow and Blue filled areas are for populations initiated for TL-1 Phase 2 and under the Top-Off funding in 2009, respectively; Red indicates work already completed during Phase 1 as part of Phase 2; Light blue and light yellow indicates new cycle being initiated for TL-1 Phase 1 ‘Top-Off’ and Phase 2 populations, respectively. Top-Off populations (SuVita2/Mouride and IT93K-503-1/IT84S-2246) currently consist of 92 F4 families each, with phenotyping being conducted at UCR, Senegal and Burkina Faso. The 6 Phase 2 MARS founder populations (Table 2) will consist of 300 F3:4 families.
  10. 10. Biparental populations to evaluate MARS # Known resistance/tolerance traits present in Cross Partner polymorphic population markers IT98K-1111-1/IT84S-2246* IITA 256 heat, multiple IT96D-610/ IT97K-499-39 IITA 114 drought, Striga KVx525/SuVita2 Burkina 143 Striga (race 1,2,3) IT84S-2246/IT93K-503-1 Burkina /UCR 143 multiple*, drought, Macrophomina Striga (races 1,2,3), bruchids, bacterial Mouride/SuVita2 Senegal/UCR 226 blight,CAbMV drought, Macrophomina, Striga (races 1,3,4), IT93K-503-1/Yacine Senegal 306 aphid, bacterial blight, CAbMV SuVita2/Melakh Mozambique 301 aphid, bacterial blight, CAbMV IT84S-2246/IT95K-1491 Mozambique 220 aphid, thrips, bruchids, multiple  Also - Phenotyping 2 populations for heat and aphid tolerance marker discovery
  11. 11. Activity 3: Employ MABC to develop improved breeding lines •  MABC to introgress/validate QTL into local varieties –  QTL validation – 4 Drought , flower thrips, Macrophomena –  MABC lines for release in TL-III
  12. 12. Activity 4. Capacity Building •  Two PhD students at UC Riverside   Senegal (Penda Sarr)   Mozambique (Arsenio Ndeve)   Jointly supported by TL-I and USAID CRSP   MABC and MARS breeding •  One PhD student at WACCI   Burkina Faso (Joseph Batieno)   GCP CB supported •  English training now •  Workshop for TL-1 and TL-2 breeders in MAS, MARS, MABC w/MBP   Use their own genotypic and phenotypic data
  13. 13. 2014 Vision for Cowpea   Modern cowpea breeding implemented •  Several African NARS •  Modern breeding strategies (e.g. MARS) evaluated •  Improved breeding lines developed, transferred to TL-III   Local varieties with enhanced performance near release •  Introgress drought tolerance, biotic stress QTL using MABC •  Released in TL-III   New tools and resources available •  A MAGIC population for cowpea research community •  New SNP-QTL markers for drought and heat tolerance plus aphid and bacterial blight resistance   Enhanced capacity in modern breeding •  3 African PhD students and 7 NARS scientists trained in modern breeding
  14. 14. Impacts:   Modernization of cowpea breeding to expedite delivery of improved varieties   Greater cowpea production in drought- prone environments   Enhanced breeding potential from: •  Elite drought tolerant breeding lines •  More powerful tools (genotyping platform, consensus map)   Increased capacity/sustainability in modern breeding •  3 African PhD students & 7 NARS scientists trained in modern breeding
  15. 15. Thank You
  16. 16. Phase II Outputs for MBP:   MAGIC population available for gene discovery   Genotypic and phenotypic data from 2 cycles of MARS   300 additional RIL genotyped, even better map Outputs for TL-III   Validated markers for Drought Tolerance, Macrophomena, Bacterial Blight, Flower Thrips & Striga resistance   More SNP markers for drought from elite x elite analysis   New markers for heat tolerance, aphid resistance   1,000 SNPs validated for use in flexible genotyping platforms   8 ‘improved local’ candidate varieties from MABC   24 advanced breeding lines from MARS