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
2010 2011 2012 2013 2014
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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