GRM 2013: Improve cowpea productivity for marginal environments in sub-Saharan Africa -- P Roberts
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
GCP General Research Meeting, Lisbon, September 2013
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 F5 – F6 seed
o Planted now to produce F6 & F7
*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
13. QTL effects on yield and seed weight
Yield-8 (1_0033)
A: Suvita-2 allele
B: IT97K-499-35 allele
0
50
100
150
200
250
300
Seedweightperplot(g)
AA
AB
BB
10
12
14
16
18
20
22
100-seedweight(g)
AA
AB
BB
GDW-11 (1_0771)
20. CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d. Heat Tolerance QTL in Elite RILs
21. Map positions of five heat tolerance QTL
Cht-1
Cht-2
Cht-3
Cht-4
Cht-5
22. CB27 (sensitive) x IT97K-556-6 (resistant)
SR
3d. Aphid Resistance QTL in Elite RILs
S
23. QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL
66%
phenotypic
variance
Minor QTL 9%
phenotypic
variance
24. 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
25. 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
26. Thank YouUniversity of
California, Riverside
Roberts, Philip A.
Close, Timothy J.
Huynh, Bao Lam
Lucas, Mitchell
Ndeve, Arsenio
Pottorff, Marti
Wanamaker, Steve
Xu, Shizhong
Hu, Zhiqui
26
National Agricultural Research System
(NARS)
Cisse, Ndiaga, ISRA-Senegal
Drabo, Issa, INERA-Burkina Faso
Tignegre, Jean-Baptiste, INERA, Burkina Faso
Rogerio Chiulele, Eduardo Mondlane U,
Mozambique
International Institute
of Tropical Agriculture
(IITA)
Boukar, Ousmane
Fatokun, Christian
Ofodile, Sam
27.
28. Validation of MAGIC population by SNP genotyping
Method
Identified 91 parent-unique SNPs
KBio genotyping
Results
2-ways (91 SNPs)
Number of crosses tested – All - 72
Number of crosses validated – all (100%)
8-ways (78 SNPs)
Assayed for presence of all four 2-ways in
parentage
Number of crosses genotyped - 368
Validation not yet complete (238 done, 126 in
progress)
Activity 1: MAGIC population
29. Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_0031
2010-057-190 F2 GG GG AA GG GG
2010-057-190-01 F4 GG GG AA GG GG
2010-057-190-02 F4 GG -- AA -- GG
2010-057-190-03 F4 GG GG AA GG GG
2010-057-190-04 F4 GG GG AA GG GG
2010-057-190-05 F4 GA GC GA GC GA
2010-057-190-06 F4 GG GG AA GG GG
2010-057-190-07 F4 GG GG AA GG GG
2010-057-190-08 F4 GG GG AA GG GG
2010-057-190-09 F4 GG GG AA GG GG
2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
31. MARS – Burkina: Genotyping 10
individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
32. Background and QTL selection within BC1F1
Striga
1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AA
IT97K-499-35 (donor) 0 BB BB BB BB BB BB
F1 50 AB AB AB AB AB AB
M499_BC1F1_12 92 AA AA AA AA AA AA
M499_BC1F1_25 88 AA AA AA AA AA AA
M499_BC1F1_43 86 AB AB AB AB AB AA
M499_BC1F1_04 85 AB AB AB AB AB AB Yes
M499_BC1F1_06 81 AA AA AA AA AA AB
M499_BC1F1_35 80 AA AA AA AA AA AA
M499_BC1F1_20 80 AB AB AB AB AB AA
M499_BC1F1_21 78 AA AA AA AA AA AB
M499_BC1F1_29 77 AA AA AA AA AA AA
M499_BC1F1_10 75 AB AB AB AB AB AB Yes
M499_BC1F1_01 75 AA AA AA AA AA AA
M499_BC1F1_73 67 AA AA AA AA AA AB
M499_BC1F1_67 64 AB AB AB AB AB AB
M499_BC1F1_28 64 AA AB AA AB AB AB
M499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID % Moussa
Selected
for BC2
Yield
33. BC2F1 plants
(Leaf samples submitted to KBiosciences. Possible BC3 crosses being
made while awaiting genotypic data)
34. 3d. QTL Discovery in Elite RILs
Heat Tolerance
– CB27 x IT82E-18
– Yield, yield components
– Phenotyped Summers 2010 & 2011
– QTL analysis in 2012
– 5 QTL discovered
– Lucas et al. 2012 Markers for
Breeding Heat Tolerant Cowpea.
Molecular Breeding 31:529-536.
38. Linkages with TL-2 Project
Genotyping and Analyses for TL-2
• 2011/12 – SNP-genotyped 321 TL-2 lines that
looked promising in multiple TL-2 drought trials
• association analysis: phenotype-genotype
• no significant QTLs observed
Identified top priorities for marker validation in
TL-2 materials – Hyderabad, October 2012
• Bacterial blight resistance
• Thrips resistance
• Aphid resistance
• Now working on MABC – common populations
Notas do Editor
I’ll be reviewing Year 1 progress on the 4 key project activities, viz…
Year 2. Crosses will be made between
Moz. new F4 family seed sent in Dec. from F3 families grown at UCR. Phenotyping ongoing, genotyping nowIITA
Everyone is welcome to add more backcross projects. What else should be added? Have to be careful not to add excessive obligations in written report. Also have to be careful to ensure success with at least a smaller number. For now, identify the two best from each breeder group.Ndiaga. Melakh x (Melakh x IT89K-499-39) (is 89 really 97?); Yacine x (Yacine x SuVita2). Issa, Jean-Baptiste, Joseph. Boukar.Rogerio.UCR. Above.
Other trainees? Boukar, yes. Cisse, yes, several. Drabo, not many but yes.
Progress was made in implementing ICIS plant breeding management software and other modern breeding support tools at UCR and IITA. In June 2010, UCR databasing expert Steve Wanamaker attended the IBP data management workshop in Zaragoza, Spain. As a result of working together in Zaragoza with Graham McLaren, cowpea breeding histories from the long-term IITA breeding program were entered into ICIS, as well as new pedigrees of crosses generated recently at UCR. However, ICIS remains difficult to use due to a nominally developed user interface and numerous bugs that have been encountered. Steve Wanamaker, Jorge Franco, TL-1 cowpea database coordinator at IITA, and project PI Jeff Ehlers also attended the TL-1 Data Management Workshop in Madrid, Spain at the end of August. Wanamaker demonstrated how the software ‘Graphviz’ (http://www.graphviz.org/) can be loaded into ICIS to greatly improve the illustrations of pedigrees. Wanamaker also participated in discussions (through a remote connection), with the IBP/iPlant Workshop in Arizona at the end of September.
Heat tolerance phenotyping was conducted in a greenhouse at UCR from July – September 2010.on 140 inbred lines of elite x elite population IT82E-18 x CB27. Aphid resistance phenotyping was conducted on 112 inbred families of elite x elite population IT97K-556-6 x CB27 in California using a specialized design with ‘spreader rows’ at a ‘hotspot’ field location from June – Sept. 2010. Data is still being analyzed from both trials at present, and although both trials appeared to provide good discrimination, additional time is needed to confirm these results and to conduct the aphid trial in Burkina Faso and Senegal to ensure the resistance observed in California is effective at these African locations.
Tanzania, Mali, Niger, Nigeria, Mozambique already part. In Mozambique does not include Rogerio. TL-1 can advocate Rogerio for Mozambique. Will add other countries for Phase II.
Heat tolerance phenotyping was conducted in a greenhouse at UCR from July – September 2010.on 140 inbred lines of elite x elite population IT82E-18 x CB27. Aphid resistance phenotyping was conducted on 112 inbred families of elite x elite population IT97K-556-6 x CB27 in California using a specialized design with ‘spreader rows’ at a ‘hotspot’ field location from June – Sept. 2010. Data is still being analyzed from both trials at present, and although both trials appeared to provide good discrimination, additional time is needed to confirm these results and to conduct the aphid trial in Burkina Faso and Senegal to ensure the resistance observed in California is effective at these African locations.
Tanzania, Mali, Niger, Nigeria, Mozambique already part. In Mozambique does not include Rogerio. TL-1 can advocate Rogerio for Mozambique. Will add other countries for Phase II.