This document outlines a draft workplan for improving cowpea productivity in marginal environments in Sub-Saharan Africa from November 2009. It involves partners across the cowpea growing region using modern breeding strategies like MARS and MABC. The workplan builds on outputs from Phase 1 including drought tolerant germplasm, markers for stress resistance, and a high density SNP map. Key activities include developing a MAGIC population, genomic resources to support marker-assisted breeding, and employing MARS and MABC over two cycles to develop improved cowpea varieties for release. The goal is to speed delivery of cowpea varieties resistant to drought, diseases and pests to improve food security.

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. 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. 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. 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. 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. 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. Activity 1: Develop MAGIC population
SNP genotypes for the eight prospec3ve parents for linkage
group 1 are shown below as an example.

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. 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
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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. 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. 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

13. 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

14. 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

15. 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

16. Thank You

17. 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