This document summarizes activities from Phase II of the Tropical Legumes 1 project, which aims to improve cowpea productivity in marginal environments in sub-Saharan Africa. Key activities included developing a multi-parent advanced generation intercross (MAGIC) population, generating genomic resources like an improved consensus map, and employing marker-assisted recurrent selection (MARS) and marker-assisted backcrossing (MABC) to develop improved cowpea lines. The project involved multiple institutions across Africa and generated important products like a MAGIC population, genomic resources, quantitative trait loci (QTL) discoveries, and preliminary advanced breeding lines.
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TLM III: Improve cowpea productivity for marginal environments in sub-Saharan Africa – O Boukar
1. Tropical Legumes 1: Objective 2
Improve cowpea productivity for marginal
environments in sub-Saharan Africa
Phil Roberts, Tim Close, Bao Lam Huynh – UC Riverside
Ndiaga Cisse, Penda Sarr - ISRA, Senegal
Issa Drabo, Jean-Baptiste Tignegre - INERA, Burkina Faso
Rogerio Chiulele, Arsenio Ndeve - E. Mondlane U, Mozambique
Ousmane Boukar, Sam Ofodile, Christian Fatokun - IITA, Nigeria
2. TL1 Phase II (June 2010 – present)
• Activity 1: Develop MAGIC population
• Activity 2: Develop genomic resources in support
of marker-assisted breeding
• Activity 3: Employ MARS and MABC to develop
improved breeding lines
• Activity 4: Capacity Building
• Activity 5: Curate and Store Phase I and II Data
3. G3: 300 4-way x 4-way intercrosses
yielding 8-way F1s; Fall 2011
G2: ~330 pair crosses made, Spring 2011
Activity 1 Product: MAGIC population
G4: Single seed descent of F2s 2012-
2013
o Most now at F6 – F7 seed
*2-ways & 8-ways SNP-validated 2012-2013
4. Activity 2 Products: Genomic resources in support
of marker-assisted breeding
a. Improved consensus map
b. Refined the GCP cowpea genotyping workflow and
supported GSS-client interactions (e.g. SNP selection)
c. Sets of markers were selected and data produced for
MARS and MABC
d. QTL discovered in 3 of 5 MARS populations - ICI
Mapping (IBP tool)
e. Breeding values & selection indices developed for
MARS individuals for intermating – OptiMAS (IBP tool)
f. QTL for heat tolerance and aphid resistance discovered
in elite populations
5. 2a. Improved Consensus Map (v6)
• 11 RIL populations
• rogues removed
• 1117 genotyped
• 1091 mapped SNPs
• 816 bins
• improved order
• clarified synteny
with other legumes
Latest version (v6) available on
www.HarvEST:Cowpea
Last published version (v4) is in Lucas
et al. 2011 Cowpea (Vu) and common
bean (Pv) synteny
7. 2b. Refined the GCP cowpea genotyping workflow
and supported GSS-client interactions
• Interacted with the GCP GSS (He, Delannay), GDMS
(McLaren, Ereful, Trushar) and KBioscience (GLC) to
streamline sample organization and data flow
• Extensive use of GLC genotyping for MARS and MABC
has led to improvements in standard operating
procedure
– Established an inventory of sample collection plates at each
breeder location
– Matched positions of samples in plates with field plot maps
– Increased all dialog to improve flow of leaf samples to GLC for
genotyping
– Improved data interpretation and application to MARS & MABC
8. Activity 3 Products: Employ MARS &
MABC; QTL Discovery
a. MARS populations for Burkina Faso, Mozambique,
Nigeria and Senegal genotyped and phenotyped
b. Continued MABC to develop improved breeding
lines – genotyping & phenotyping
c. Implemented MAB tools (OptiMAS, ICI mapping),
training on beta versions of Fieldbook
d. QTL for heat tolerance and aphid resistance
discovered in elite populations
9. Institution Population SNPs Current Stage
INERA, Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA, Nigeria
IT84S-2246 x IT98K-1111-1
IT97K-499-35 x IT93K-503-1
102
95
Cycle 1 Intercross
Terminated
EMU, Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA, Senegal IT93K-503-1 x Mouride 136 Adjusted, Now F2:F6
3a. MARS Breeding Progress
11. Example: Traits measured in
250 F2:3 families at two field sites
in Burkina Faso; Issa Drabo
Set#2
Traits 140 lines, <100 seeds/line
Pobe Saria Saria
Number of plants
Maturity
Flowering time
Virus symptoms
Pod weight/plot
Seed weight/plot
100-seed weight
Set#1
110 lines, >=100 seeds/line
12. 0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LODScore
QTLs from ICI Mapping –
Burkina Faso, Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
18. CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d. Heat tolerance QTL identified in elite RILs
19. CB27 (sensitive) x IT97K-556-6 (resistant)
SR
3d. Aphid resistance QTL identified in elite RILs
S
20. Activity 4 Products. Capacity Building
Two PhD students
• Senegal (Penda Sarr – enrolled 2011 at Anta Diop Chiekh
University, Dakar, Senegal)
• Mozambique (Arsenio Ndeve – enrolled Winter 2012 at UCR)
• Jointly supported by GCP and USAID CRSP
• MABC and MARS breeding
PhD students at WACCI
• Burkina Faso (Joseph Batieno) – MABC project;
supported by GCP Capacity Building funds
• Ken Fafa – using KBio SNPs for cowpea seed size
MSc students at E. Mondlane U, Mozambique
• Mentoring in plant breeding with Rogerio Chiulele
21. Activity 5 Products: Data Curation & Storage
• TL-1 datasets
– Provided genotype datasets to GCP curators (Trushar)
• 1536-SNP Illumina platform
• ~650 germplasm accessions
• Includes almost all MARS and MABC parents
– Organized phenotype datasets: UCR in collaboration
with Sam Ofodile at IITA
• uniform naming conventions, file structure, error detection
• 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
– Added historical pedigrees of IITA lines & pedigrees of
TL-1 materials to IITA/GCP database