1. TL-I Objective 2 Phase 2 Draft Workplan â Nov. 20, 2009
âImproving Cowpea Productivity for Marginal
Environments in SSAâ
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. Partners located across semi-arid âcowpea zoneâ:
IITA â 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. Rationale
ďâ Cowpea is a key component of
cropping systems, food security in SSA
ďâ Cowpea productivity impacted by:
â˘âDrought, heat; Macrophomena, bacterial
blight, flower thrips, aphids, Striga,nematodes
ďâ Solution â Cowpea varieties that resist
these stresses
ďâ âModern Breedingâ speeds delivery
â˘â Apply the outputs of current TL-1 in new
breeding strategies (MARS, MABC)
â˘â Transfer Phase I outputs to TL-2
ďźâ High-throughput SNP genotyping
ďźâ Markers for drought and biotic stress resistance
ďźâ Agarose-gel based markers from SNPs
5. Phase 2 will build on current
outputs of TL-1 & TL-2
ďâ Drought tolerant germplasm and
drought QTL identified
ďâ Key QTL for resistance to flower thrips,
Macrophomina, root-knot nematode
ďâ High-throughput SNP genotyping
â˘â Essential tool for MARS, MABC
â˘â Select single-plex SNPsâ custom assays
ďâ High density SNP consensus map
(Muchero et al., PNAS, 2009)
680cM; 11 LG; 1 marker/0.7cM
5Â
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
8. Activity 2: Develop genomic resources in support of
marker-assisted breeding
â˘â Customized sets of markers for MARS ; genotype
data production in support of MARS breeding
â˘â Genotyping data analysis to optimize MARS
(breeding values, selection indices)
â˘â Genetic analysis for QTL discovery in MARS
populations
9. Activity 3: Employ MARS and MABC to develop
improved breeding lines
â˘â 2 populations per partner, 300 lines/population
â˘â Conduct MARS cycles 1 and 2 in elite x elite crosses
â˘â 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 âTop-Offâ 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.
11. Activity 3: Employ MABC to develop improved
breeding lines
â˘â MABC to introgress/validate QTL into local varieties
ââ QTL validation â 4 Drought , flower thrips, Macrophomena
ââ MABC lines for release in TL-III
12.
13. Activity 4. Capacity Building
â˘â Two PhD students at UC Riverside
ďâ Senegal (Penda Sarr)
ďâ Mozambique (Arsenio Ndeve)
ďâ Jointly supported by TL-I and USAID CRSP
ďâ MABC and MARS breeding
â˘â One PhD student at WACCI
ďâ Burkina Faso (Joseph Batieno)
ďâ GCP CB supported
â˘â English training now
â˘â Workshop for TL-1 and TL-2 breeders in
MAS, MARS, MABC w/MBP
ďâ Use their own genotypic and phenotypic data
14. 2014 Vision for Cowpea
ďâ Modern cowpea breeding implemented
â˘â Several African NARS
â˘â Modern breeding strategies (e.g. MARS) evaluated
â˘â Improved breeding lines developed, transferred to TL-III
ďâ Local varieties with enhanced performance near release
â˘â Introgress drought tolerance, biotic stress QTL using MABC
â˘â Released in TL-III
ďâ New tools and resources available
â˘â A MAGIC population for cowpea research community
â˘â New SNP-QTL markers for drought and heat tolerance plus aphid
and bacterial blight resistance
ďâ Enhanced capacity in modern breeding
â˘â 3 African PhD students and 7 NARS scientists
trained in modern breeding
15. Impacts:
ďâ Modernization of cowpea breeding to
expedite delivery of improved varieties
ďâ Greater cowpea production in drought-
prone environments
ďâ Enhanced breeding potential from:
â˘â Elite drought tolerant breeding lines
â˘â More powerful tools (genotyping platform,
consensus map)
ďâ Increased capacity/sustainability in modern
breeding
â˘â 3 African PhD students & 7 NARS scientists
trained in modern breeding
17. Phase II Outputs for MBP:
ďâ MAGIC population available for gene discovery
ďâ Genotypic and phenotypic data from 2 cycles of MARS
ďâ 300 additional RIL genotyped, even better map
Outputs for TL-III
ďâ Validated markers for Drought Tolerance, Macrophomena,
Bacterial Blight, Flower Thrips & Striga resistance
ďâ More SNP markers for drought from elite x elite analysis
ďâ New markers for heat tolerance, aphid resistance
ďâ 1,000 SNPs validated for use in flexible genotyping platforms
ďâ 8 âimproved localâ candidate varieties from MABC
ďâ 24 advanced breeding lines from MARS