grm 2011: improving cowpea productivity in africa - j ehlers
TRANSCRIPT
Phase II Activities and Highlights
Tropical Legume 1 Objective 2
Improving cowpea productivity for marginal
environments in Africa
Jeff Ehlers Phil Roberts Tim Close Zhiqiu Hu - UC Riverside
Ndiaga Cisse ISRA Senegal
Issa Drabo Jean-Baptist Tignegre - INERA Burkina Faso
Rogerio Chiulele - Eduardo Mondlane Univ Mozambique
Ousmane Boukar Jorge Franco Sam Ofodile- IITA Nigeria
GCP-GRM ICRISAT Hyderabad September 252011
Building on Phase I Key Outputs
bull 4 Key Resources for Modern Breeding Developed
ndash 1 high-throughput genotyping platform
bull Based on Illumina 1536 GoldenGate Assay
ndash 2 high quality consensus genetic map
bull 6 RILs 741 lines 928 markers
ndash 3 fingerprints of gt500 parental lines
bull 370 IITAGCP mini-core
bull 200 IITA West African linescultivars
ndash 4 QTL and trait-linked markers
bull Drought tolerance
bull Resistance to flower and foliar thrips ashy-stem blight bacterial
blight root-knot nematodes
Phase II Activities Highlights
bull Activity 1 Develop MAGIC population
bull Activity 2 Develop genomic resources in
support of marker-assisted breeding
bull Activity 3 Employ MARS and MABC to develop
improved breeding lines
bull Activity 4 Capacity Building
bull Activity 5 Curate and Store Phase I and II Data
2 DC 360 double cross seed each
4-way (ABCD and EFGH) Fall 2010
4 single crosses Spring 2010
Develop MAGIC population
300+ 8-way individuals formed
being intercrossed now
8 diverse parents chosen
- NJ analysis
- traits
Available on
wwwHarvESTcowpea Lucas et al
The Genome (in press)
New Cowpea
Consensus Map
bull 11 RILs 2 F4
bull 1293 genotyped
bull 1107 mapped
SNPs
bull 856 bins
bull 33 more bins
bull 19 more markers
bull improved order
1_0502 1_1360 1_0504 1_1499 1_1138 1_1413 1_0847 1_0774 1_1221 1_0027 1_0153 1_0535 1_1092 1_0646
AA AA CC CC AA TT -- TT AA AA AA GG AA TT
GG TT TT TT GG GG -- CC GG GG GG AA GG AA
AA AA CC CC AA TT AA TT AA AA AA GG AA TT
GG TT TT TT GG GG TT CC GG GG GG AA GG AA
Linkage group
3 4 5 6
LO
D
0
2
4
6
8
10(c-1)
Linkage group
3 4 5 6
0
2
4
6
8
10(c-2)
(a-1)
(a-2)
(b)
lsquoPhase Checkerrsquo software to improve map and QTL ID
Bioinformatics
(submitted)
GenomeStudio
Output 5 lines
Corrected
Output
Inferred
parental
Parental
data
Selecting customized sets of markers for KASPAR
bull With high density genotyping
ndash Many markers polymorphic in
a given cross are tightly linked
ndash no need to genotype all in
breeding
bull Marker selection by hand ndash slow amp
laborious when 200+ candidate
markers
bull How to efficiently choose
lsquobackgroundrsquo and trait-linked
markers for given cross to get a
cost-optimized marker set for
KASPAR genotyping
SNP LG cM IT93K-503-1 IT84S-2246 Polymorphic
1_0190 4 683 AA AA 0
1_0502 4 1027 BB AA 1
1_1148 4 1036 AA AA 0
1_0382 4 1066 AA AA 0
1_1360 4 1223 BB AA 1
1_0504 4 1276 AA BB 1
1_1499 4 1369 AA BB 1
1_1138 4 1409 BB AA 1
1_0155 4 1556 BB BB 0
1_0082 4 1797 AA AA 0
1_0756 4 1837 AA AA 0
1_1413 4 1838 BB AA 1
1_1445 4 191 BB BB 0
1_0847 4 1948 -- -- 0
1_0774 4 2016 BB AA 1
1_1221 4 2016 BB AA 1
1_1242 4 2072 BB BB 0
1_0027 4 2149 BB AA 1
1_0153 4 2149 BB AA 1
1_0535 4 2285 AA BB 1
1_1261 4 2292 BB BB 0
1_1092 4 2366 BB AA 1
1_0646 4 2412 BB AA 1
1_0874 4 244 AA BB 1
1_1264 4 2443 -- -- 0
1_0826 4 2455 BB AA 1
1_0692 4 25 AA BB 1
1_0403 4 2531 -- AA 0
1_0106 4 2557 AA BB 1
1_0678 4 276 BB AA 1
1_1209 4 279 -- BB 0
lsquoBreedItrsquo
bull Program to choose a marker set for a given cross
ndash Input SNP data table (genotype or locus file)
ndash Input trait (QTL markers) and map files
ndash Program Options
bull Choose 2 parents
bull Choose cM interval for background selection
bull Choose cM interval for markers flanking traits
bull Output list of SNPs for KBiosciences assay
bull Can quickly compare cost versus marker density
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Building on Phase I Key Outputs
bull 4 Key Resources for Modern Breeding Developed
ndash 1 high-throughput genotyping platform
bull Based on Illumina 1536 GoldenGate Assay
ndash 2 high quality consensus genetic map
bull 6 RILs 741 lines 928 markers
ndash 3 fingerprints of gt500 parental lines
bull 370 IITAGCP mini-core
bull 200 IITA West African linescultivars
ndash 4 QTL and trait-linked markers
bull Drought tolerance
bull Resistance to flower and foliar thrips ashy-stem blight bacterial
blight root-knot nematodes
Phase II Activities Highlights
bull Activity 1 Develop MAGIC population
bull Activity 2 Develop genomic resources in
support of marker-assisted breeding
bull Activity 3 Employ MARS and MABC to develop
improved breeding lines
bull Activity 4 Capacity Building
bull Activity 5 Curate and Store Phase I and II Data
2 DC 360 double cross seed each
4-way (ABCD and EFGH) Fall 2010
4 single crosses Spring 2010
Develop MAGIC population
300+ 8-way individuals formed
being intercrossed now
8 diverse parents chosen
- NJ analysis
- traits
Available on
wwwHarvESTcowpea Lucas et al
The Genome (in press)
New Cowpea
Consensus Map
bull 11 RILs 2 F4
bull 1293 genotyped
bull 1107 mapped
SNPs
bull 856 bins
bull 33 more bins
bull 19 more markers
bull improved order
1_0502 1_1360 1_0504 1_1499 1_1138 1_1413 1_0847 1_0774 1_1221 1_0027 1_0153 1_0535 1_1092 1_0646
AA AA CC CC AA TT -- TT AA AA AA GG AA TT
GG TT TT TT GG GG -- CC GG GG GG AA GG AA
AA AA CC CC AA TT AA TT AA AA AA GG AA TT
GG TT TT TT GG GG TT CC GG GG GG AA GG AA
Linkage group
3 4 5 6
LO
D
0
2
4
6
8
10(c-1)
Linkage group
3 4 5 6
0
2
4
6
8
10(c-2)
(a-1)
(a-2)
(b)
lsquoPhase Checkerrsquo software to improve map and QTL ID
Bioinformatics
(submitted)
GenomeStudio
Output 5 lines
Corrected
Output
Inferred
parental
Parental
data
Selecting customized sets of markers for KASPAR
bull With high density genotyping
ndash Many markers polymorphic in
a given cross are tightly linked
ndash no need to genotype all in
breeding
bull Marker selection by hand ndash slow amp
laborious when 200+ candidate
markers
bull How to efficiently choose
lsquobackgroundrsquo and trait-linked
markers for given cross to get a
cost-optimized marker set for
KASPAR genotyping
SNP LG cM IT93K-503-1 IT84S-2246 Polymorphic
1_0190 4 683 AA AA 0
1_0502 4 1027 BB AA 1
1_1148 4 1036 AA AA 0
1_0382 4 1066 AA AA 0
1_1360 4 1223 BB AA 1
1_0504 4 1276 AA BB 1
1_1499 4 1369 AA BB 1
1_1138 4 1409 BB AA 1
1_0155 4 1556 BB BB 0
1_0082 4 1797 AA AA 0
1_0756 4 1837 AA AA 0
1_1413 4 1838 BB AA 1
1_1445 4 191 BB BB 0
1_0847 4 1948 -- -- 0
1_0774 4 2016 BB AA 1
1_1221 4 2016 BB AA 1
1_1242 4 2072 BB BB 0
1_0027 4 2149 BB AA 1
1_0153 4 2149 BB AA 1
1_0535 4 2285 AA BB 1
1_1261 4 2292 BB BB 0
1_1092 4 2366 BB AA 1
1_0646 4 2412 BB AA 1
1_0874 4 244 AA BB 1
1_1264 4 2443 -- -- 0
1_0826 4 2455 BB AA 1
1_0692 4 25 AA BB 1
1_0403 4 2531 -- AA 0
1_0106 4 2557 AA BB 1
1_0678 4 276 BB AA 1
1_1209 4 279 -- BB 0
lsquoBreedItrsquo
bull Program to choose a marker set for a given cross
ndash Input SNP data table (genotype or locus file)
ndash Input trait (QTL markers) and map files
ndash Program Options
bull Choose 2 parents
bull Choose cM interval for background selection
bull Choose cM interval for markers flanking traits
bull Output list of SNPs for KBiosciences assay
bull Can quickly compare cost versus marker density
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Phase II Activities Highlights
bull Activity 1 Develop MAGIC population
bull Activity 2 Develop genomic resources in
support of marker-assisted breeding
bull Activity 3 Employ MARS and MABC to develop
improved breeding lines
bull Activity 4 Capacity Building
bull Activity 5 Curate and Store Phase I and II Data
2 DC 360 double cross seed each
4-way (ABCD and EFGH) Fall 2010
4 single crosses Spring 2010
Develop MAGIC population
300+ 8-way individuals formed
being intercrossed now
8 diverse parents chosen
- NJ analysis
- traits
Available on
wwwHarvESTcowpea Lucas et al
The Genome (in press)
New Cowpea
Consensus Map
bull 11 RILs 2 F4
bull 1293 genotyped
bull 1107 mapped
SNPs
bull 856 bins
bull 33 more bins
bull 19 more markers
bull improved order
1_0502 1_1360 1_0504 1_1499 1_1138 1_1413 1_0847 1_0774 1_1221 1_0027 1_0153 1_0535 1_1092 1_0646
AA AA CC CC AA TT -- TT AA AA AA GG AA TT
GG TT TT TT GG GG -- CC GG GG GG AA GG AA
AA AA CC CC AA TT AA TT AA AA AA GG AA TT
GG TT TT TT GG GG TT CC GG GG GG AA GG AA
Linkage group
3 4 5 6
LO
D
0
2
4
6
8
10(c-1)
Linkage group
3 4 5 6
0
2
4
6
8
10(c-2)
(a-1)
(a-2)
(b)
lsquoPhase Checkerrsquo software to improve map and QTL ID
Bioinformatics
(submitted)
GenomeStudio
Output 5 lines
Corrected
Output
Inferred
parental
Parental
data
Selecting customized sets of markers for KASPAR
bull With high density genotyping
ndash Many markers polymorphic in
a given cross are tightly linked
ndash no need to genotype all in
breeding
bull Marker selection by hand ndash slow amp
laborious when 200+ candidate
markers
bull How to efficiently choose
lsquobackgroundrsquo and trait-linked
markers for given cross to get a
cost-optimized marker set for
KASPAR genotyping
SNP LG cM IT93K-503-1 IT84S-2246 Polymorphic
1_0190 4 683 AA AA 0
1_0502 4 1027 BB AA 1
1_1148 4 1036 AA AA 0
1_0382 4 1066 AA AA 0
1_1360 4 1223 BB AA 1
1_0504 4 1276 AA BB 1
1_1499 4 1369 AA BB 1
1_1138 4 1409 BB AA 1
1_0155 4 1556 BB BB 0
1_0082 4 1797 AA AA 0
1_0756 4 1837 AA AA 0
1_1413 4 1838 BB AA 1
1_1445 4 191 BB BB 0
1_0847 4 1948 -- -- 0
1_0774 4 2016 BB AA 1
1_1221 4 2016 BB AA 1
1_1242 4 2072 BB BB 0
1_0027 4 2149 BB AA 1
1_0153 4 2149 BB AA 1
1_0535 4 2285 AA BB 1
1_1261 4 2292 BB BB 0
1_1092 4 2366 BB AA 1
1_0646 4 2412 BB AA 1
1_0874 4 244 AA BB 1
1_1264 4 2443 -- -- 0
1_0826 4 2455 BB AA 1
1_0692 4 25 AA BB 1
1_0403 4 2531 -- AA 0
1_0106 4 2557 AA BB 1
1_0678 4 276 BB AA 1
1_1209 4 279 -- BB 0
lsquoBreedItrsquo
bull Program to choose a marker set for a given cross
ndash Input SNP data table (genotype or locus file)
ndash Input trait (QTL markers) and map files
ndash Program Options
bull Choose 2 parents
bull Choose cM interval for background selection
bull Choose cM interval for markers flanking traits
bull Output list of SNPs for KBiosciences assay
bull Can quickly compare cost versus marker density
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
2 DC 360 double cross seed each
4-way (ABCD and EFGH) Fall 2010
4 single crosses Spring 2010
Develop MAGIC population
300+ 8-way individuals formed
being intercrossed now
8 diverse parents chosen
- NJ analysis
- traits
Available on
wwwHarvESTcowpea Lucas et al
The Genome (in press)
New Cowpea
Consensus Map
bull 11 RILs 2 F4
bull 1293 genotyped
bull 1107 mapped
SNPs
bull 856 bins
bull 33 more bins
bull 19 more markers
bull improved order
1_0502 1_1360 1_0504 1_1499 1_1138 1_1413 1_0847 1_0774 1_1221 1_0027 1_0153 1_0535 1_1092 1_0646
AA AA CC CC AA TT -- TT AA AA AA GG AA TT
GG TT TT TT GG GG -- CC GG GG GG AA GG AA
AA AA CC CC AA TT AA TT AA AA AA GG AA TT
GG TT TT TT GG GG TT CC GG GG GG AA GG AA
Linkage group
3 4 5 6
LO
D
0
2
4
6
8
10(c-1)
Linkage group
3 4 5 6
0
2
4
6
8
10(c-2)
(a-1)
(a-2)
(b)
lsquoPhase Checkerrsquo software to improve map and QTL ID
Bioinformatics
(submitted)
GenomeStudio
Output 5 lines
Corrected
Output
Inferred
parental
Parental
data
Selecting customized sets of markers for KASPAR
bull With high density genotyping
ndash Many markers polymorphic in
a given cross are tightly linked
ndash no need to genotype all in
breeding
bull Marker selection by hand ndash slow amp
laborious when 200+ candidate
markers
bull How to efficiently choose
lsquobackgroundrsquo and trait-linked
markers for given cross to get a
cost-optimized marker set for
KASPAR genotyping
SNP LG cM IT93K-503-1 IT84S-2246 Polymorphic
1_0190 4 683 AA AA 0
1_0502 4 1027 BB AA 1
1_1148 4 1036 AA AA 0
1_0382 4 1066 AA AA 0
1_1360 4 1223 BB AA 1
1_0504 4 1276 AA BB 1
1_1499 4 1369 AA BB 1
1_1138 4 1409 BB AA 1
1_0155 4 1556 BB BB 0
1_0082 4 1797 AA AA 0
1_0756 4 1837 AA AA 0
1_1413 4 1838 BB AA 1
1_1445 4 191 BB BB 0
1_0847 4 1948 -- -- 0
1_0774 4 2016 BB AA 1
1_1221 4 2016 BB AA 1
1_1242 4 2072 BB BB 0
1_0027 4 2149 BB AA 1
1_0153 4 2149 BB AA 1
1_0535 4 2285 AA BB 1
1_1261 4 2292 BB BB 0
1_1092 4 2366 BB AA 1
1_0646 4 2412 BB AA 1
1_0874 4 244 AA BB 1
1_1264 4 2443 -- -- 0
1_0826 4 2455 BB AA 1
1_0692 4 25 AA BB 1
1_0403 4 2531 -- AA 0
1_0106 4 2557 AA BB 1
1_0678 4 276 BB AA 1
1_1209 4 279 -- BB 0
lsquoBreedItrsquo
bull Program to choose a marker set for a given cross
ndash Input SNP data table (genotype or locus file)
ndash Input trait (QTL markers) and map files
ndash Program Options
bull Choose 2 parents
bull Choose cM interval for background selection
bull Choose cM interval for markers flanking traits
bull Output list of SNPs for KBiosciences assay
bull Can quickly compare cost versus marker density
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Available on
wwwHarvESTcowpea Lucas et al
The Genome (in press)
New Cowpea
Consensus Map
bull 11 RILs 2 F4
bull 1293 genotyped
bull 1107 mapped
SNPs
bull 856 bins
bull 33 more bins
bull 19 more markers
bull improved order
1_0502 1_1360 1_0504 1_1499 1_1138 1_1413 1_0847 1_0774 1_1221 1_0027 1_0153 1_0535 1_1092 1_0646
AA AA CC CC AA TT -- TT AA AA AA GG AA TT
GG TT TT TT GG GG -- CC GG GG GG AA GG AA
AA AA CC CC AA TT AA TT AA AA AA GG AA TT
GG TT TT TT GG GG TT CC GG GG GG AA GG AA
Linkage group
3 4 5 6
LO
D
0
2
4
6
8
10(c-1)
Linkage group
3 4 5 6
0
2
4
6
8
10(c-2)
(a-1)
(a-2)
(b)
lsquoPhase Checkerrsquo software to improve map and QTL ID
Bioinformatics
(submitted)
GenomeStudio
Output 5 lines
Corrected
Output
Inferred
parental
Parental
data
Selecting customized sets of markers for KASPAR
bull With high density genotyping
ndash Many markers polymorphic in
a given cross are tightly linked
ndash no need to genotype all in
breeding
bull Marker selection by hand ndash slow amp
laborious when 200+ candidate
markers
bull How to efficiently choose
lsquobackgroundrsquo and trait-linked
markers for given cross to get a
cost-optimized marker set for
KASPAR genotyping
SNP LG cM IT93K-503-1 IT84S-2246 Polymorphic
1_0190 4 683 AA AA 0
1_0502 4 1027 BB AA 1
1_1148 4 1036 AA AA 0
1_0382 4 1066 AA AA 0
1_1360 4 1223 BB AA 1
1_0504 4 1276 AA BB 1
1_1499 4 1369 AA BB 1
1_1138 4 1409 BB AA 1
1_0155 4 1556 BB BB 0
1_0082 4 1797 AA AA 0
1_0756 4 1837 AA AA 0
1_1413 4 1838 BB AA 1
1_1445 4 191 BB BB 0
1_0847 4 1948 -- -- 0
1_0774 4 2016 BB AA 1
1_1221 4 2016 BB AA 1
1_1242 4 2072 BB BB 0
1_0027 4 2149 BB AA 1
1_0153 4 2149 BB AA 1
1_0535 4 2285 AA BB 1
1_1261 4 2292 BB BB 0
1_1092 4 2366 BB AA 1
1_0646 4 2412 BB AA 1
1_0874 4 244 AA BB 1
1_1264 4 2443 -- -- 0
1_0826 4 2455 BB AA 1
1_0692 4 25 AA BB 1
1_0403 4 2531 -- AA 0
1_0106 4 2557 AA BB 1
1_0678 4 276 BB AA 1
1_1209 4 279 -- BB 0
lsquoBreedItrsquo
bull Program to choose a marker set for a given cross
ndash Input SNP data table (genotype or locus file)
ndash Input trait (QTL markers) and map files
ndash Program Options
bull Choose 2 parents
bull Choose cM interval for background selection
bull Choose cM interval for markers flanking traits
bull Output list of SNPs for KBiosciences assay
bull Can quickly compare cost versus marker density
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
1_0502 1_1360 1_0504 1_1499 1_1138 1_1413 1_0847 1_0774 1_1221 1_0027 1_0153 1_0535 1_1092 1_0646
AA AA CC CC AA TT -- TT AA AA AA GG AA TT
GG TT TT TT GG GG -- CC GG GG GG AA GG AA
AA AA CC CC AA TT AA TT AA AA AA GG AA TT
GG TT TT TT GG GG TT CC GG GG GG AA GG AA
Linkage group
3 4 5 6
LO
D
0
2
4
6
8
10(c-1)
Linkage group
3 4 5 6
0
2
4
6
8
10(c-2)
(a-1)
(a-2)
(b)
lsquoPhase Checkerrsquo software to improve map and QTL ID
Bioinformatics
(submitted)
GenomeStudio
Output 5 lines
Corrected
Output
Inferred
parental
Parental
data
Selecting customized sets of markers for KASPAR
bull With high density genotyping
ndash Many markers polymorphic in
a given cross are tightly linked
ndash no need to genotype all in
breeding
bull Marker selection by hand ndash slow amp
laborious when 200+ candidate
markers
bull How to efficiently choose
lsquobackgroundrsquo and trait-linked
markers for given cross to get a
cost-optimized marker set for
KASPAR genotyping
SNP LG cM IT93K-503-1 IT84S-2246 Polymorphic
1_0190 4 683 AA AA 0
1_0502 4 1027 BB AA 1
1_1148 4 1036 AA AA 0
1_0382 4 1066 AA AA 0
1_1360 4 1223 BB AA 1
1_0504 4 1276 AA BB 1
1_1499 4 1369 AA BB 1
1_1138 4 1409 BB AA 1
1_0155 4 1556 BB BB 0
1_0082 4 1797 AA AA 0
1_0756 4 1837 AA AA 0
1_1413 4 1838 BB AA 1
1_1445 4 191 BB BB 0
1_0847 4 1948 -- -- 0
1_0774 4 2016 BB AA 1
1_1221 4 2016 BB AA 1
1_1242 4 2072 BB BB 0
1_0027 4 2149 BB AA 1
1_0153 4 2149 BB AA 1
1_0535 4 2285 AA BB 1
1_1261 4 2292 BB BB 0
1_1092 4 2366 BB AA 1
1_0646 4 2412 BB AA 1
1_0874 4 244 AA BB 1
1_1264 4 2443 -- -- 0
1_0826 4 2455 BB AA 1
1_0692 4 25 AA BB 1
1_0403 4 2531 -- AA 0
1_0106 4 2557 AA BB 1
1_0678 4 276 BB AA 1
1_1209 4 279 -- BB 0
lsquoBreedItrsquo
bull Program to choose a marker set for a given cross
ndash Input SNP data table (genotype or locus file)
ndash Input trait (QTL markers) and map files
ndash Program Options
bull Choose 2 parents
bull Choose cM interval for background selection
bull Choose cM interval for markers flanking traits
bull Output list of SNPs for KBiosciences assay
bull Can quickly compare cost versus marker density
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Selecting customized sets of markers for KASPAR
bull With high density genotyping
ndash Many markers polymorphic in
a given cross are tightly linked
ndash no need to genotype all in
breeding
bull Marker selection by hand ndash slow amp
laborious when 200+ candidate
markers
bull How to efficiently choose
lsquobackgroundrsquo and trait-linked
markers for given cross to get a
cost-optimized marker set for
KASPAR genotyping
SNP LG cM IT93K-503-1 IT84S-2246 Polymorphic
1_0190 4 683 AA AA 0
1_0502 4 1027 BB AA 1
1_1148 4 1036 AA AA 0
1_0382 4 1066 AA AA 0
1_1360 4 1223 BB AA 1
1_0504 4 1276 AA BB 1
1_1499 4 1369 AA BB 1
1_1138 4 1409 BB AA 1
1_0155 4 1556 BB BB 0
1_0082 4 1797 AA AA 0
1_0756 4 1837 AA AA 0
1_1413 4 1838 BB AA 1
1_1445 4 191 BB BB 0
1_0847 4 1948 -- -- 0
1_0774 4 2016 BB AA 1
1_1221 4 2016 BB AA 1
1_1242 4 2072 BB BB 0
1_0027 4 2149 BB AA 1
1_0153 4 2149 BB AA 1
1_0535 4 2285 AA BB 1
1_1261 4 2292 BB BB 0
1_1092 4 2366 BB AA 1
1_0646 4 2412 BB AA 1
1_0874 4 244 AA BB 1
1_1264 4 2443 -- -- 0
1_0826 4 2455 BB AA 1
1_0692 4 25 AA BB 1
1_0403 4 2531 -- AA 0
1_0106 4 2557 AA BB 1
1_0678 4 276 BB AA 1
1_1209 4 279 -- BB 0
lsquoBreedItrsquo
bull Program to choose a marker set for a given cross
ndash Input SNP data table (genotype or locus file)
ndash Input trait (QTL markers) and map files
ndash Program Options
bull Choose 2 parents
bull Choose cM interval for background selection
bull Choose cM interval for markers flanking traits
bull Output list of SNPs for KBiosciences assay
bull Can quickly compare cost versus marker density
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
lsquoBreedItrsquo
bull Program to choose a marker set for a given cross
ndash Input SNP data table (genotype or locus file)
ndash Input trait (QTL markers) and map files
ndash Program Options
bull Choose 2 parents
bull Choose cM interval for background selection
bull Choose cM interval for markers flanking traits
bull Output list of SNPs for KBiosciences assay
bull Can quickly compare cost versus marker density
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
SNP SNP_ID LG cM IT93K-503-1
IT84S-
2246 Polymorphic Trait Selected Reason Distance
1_0190 16480_663 4 683 AA AA 0 0
1_0502 5268_412 4 1027 BB AA 1 1 Every 5 cM
1_1148 10853_451 4 1036 AA AA 0 0
1_0382 6867_337 4 1066 AA AA 0 0
1_1360 12393_305 4 1223 BB AA 1 0
1_0504 14303_873 4 1276 AA BB 1 0
1_1499 12324_917 4 1369 AA BB 1 1 Flanking 341
1_1138 17303_348 4 1409 BB AA 1 Flower Thrips 1 Trait 04
1_0155 474_351 4 1556 BB BB 0 0
1_0082 13873_544 4 1797 AA AA 0 0
1_0756 14622_2490 4 1837 AA AA 0 0
1_1413 1078_282 4 1838 BB AA 1 1 Flanking 429
1_1445 13794_319 4 191 BB BB 0 0
1_0847 8899_1022 4 1948 -- -- 0 0
1_0774 16646_118 4 2016 BB AA 1 0
1_1221 1202_1215 4 2016 BB AA 1 1 Flanking 177
1_1242 4217_685 4 2072 BB BB 0 Foliar Thrips 0
1_0027 3683_549 4 2149 BB AA 1 1 Flanking 134
1_0153 14462_1712 4 2149 BB AA 1 0
1_0535 1808_342 4 2285 AA BB 1 0
1_1261 11736_560 4 2292 BB BB 0 0
1_1092 5061_428 4 2366 BB AA 1 0
1_0646 12854_535 4 2412 BB AA 1 0
1_0874 7102_965 4 244 AA BB 1 0
1_1264 11709_707 4 2443 -- -- 0 0
1_0826 9147_1655 4 2455 BB AA 1 0
1_0692 8273_1205 4 25 AA BB 1 0
1_0403 4774_665 4 2531 -- AA 0 0
1_0106 8625_1231 4 2557 AA BB 1 0
1_0678 13269_270 4 276 BB AA 1 1 Every 5 cM 611
BreedIt
output
file for
marker
selection
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Activity 3 Main MARS Breeding Effort
bull F1 made (March ndashJune 2010)
bull F1 grown out to produce F2 (Sept ndash Nov 2010)
bull F2 seed (500cross) sent to partners Feb 2011
bull Harvested ~300 plantspopln
ndash Tissue samples taken mailed to KBio
Currently F3s being phenotyped (Senegal Burkina IITA
January 2012-Mozambique)
Fall 2011 - Calculate breeding values with OptiMAS
bull Apply 10 selection intensity genotype 10
individualsfamily and intermate
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
MABC to develop improved breeding lines
Made F1 - Spring 2010 and BC1F1 Fall 2010
Made BC2F1 and BC1F2 ndash Spring 2011
Currently Phenotyping BC1F2 families for Striga tolerance (IITA
and BF)
Genotype at KBio ndash Dec 2011
Cross number
Cross No
BC1F1 Donor Traits
2011-052 IT84S-2246IT93K-503-1IT84S-2246 48 Drought Tol Striga
2011-053 IT84S-2246IT98K-1111-1IT84S-2246 48 Heat Tol Striga
2011-054 SuVita 2IT93K-503-1SuVita 2 48 Drought Tol Striga
2011-055 SuVita 2IT97K-499-35SuVita 2 48 Drought Tol Striga
Several other MABC efforts at BC1F1 stage
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
QTL Discovery in Elite RILs
bull Heat Tolerance Phenotyping
ndash Greenhouse Aug ndash Oct 2010 and 2011
ndash RIL CB27 x IT82E-18
bull Aphid Resistance Phenotyping
ndash Field hotspot Calif Summer 2010 amp11
ndash RIL CB27 x IT97K-556-6
bull Anthracnose Phenotyping
bull Burkina Faso RIL 524BIT84S-2049
Aphid Resistance QTL
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
IT93K-503xCB46 RIL
2006CVS(57)
2006UCR(57)
2007CVS(57)
2007CVS(124)
2007UCR(57)
2008CVS(91)
2008UCR(108)
VuLG4
VuLG2
VuLG8
VuLG10
Foliar Thrip Res QTL Validation LODgt84
LODgt68
LODgt4
LODgt32
Validating with
CB27IT82E-18 RIL
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
SNP SNP SNP SNP
Line Rank All Weight UC No(++) No(--) No(+-) 1_0589 1_0853 1_0604 1_1482
05066-004 1 1 1 4 4 0 0 1 1 1 1
05066-065 2 1 1 4 4 0 0 1 1 1 1
05066-109 3 0875 094 4 3 0 1 1 1 1 05
05066-001 4 075 088 3 3 1 0 1 1 1 0
05066-073 5 075 088 3 3 1 0 1 1 1 0
05066-087 6 075 088 3 3 1 0 1 1 1 0
05066-045 7 075 087 371 2 0 2 05 1 1 05
05066-103 8 075 087 3 3 1 0 0 1 1 1
05066-015 85 025 012 1 1 3 0 1 0 0 0
Mouride 86 025 012 1 1 3 0 1 0 0 0
05066-002 87 025 012 171 0 2 2 05 0 0 05
05066-034 88 025 012 1 1 3 0 0 0 0 1
05066-054 89 0125 006 1 0 3 1 0 0 0 05
05066-100 90 0 0 0 0 4 0 0 0 0 0
05066-129 91 0 0 0 0 4 0 0 0 0 0
PV 4665 1905 1015 457
Favorable DT SNPs
Drought QTL Validation
OptiMAS Results - one Pilot MARS Popln
10 best and worst lines from 3 HixHi populations
Being phenotyped now
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Bayesian QTL detection methods
being tried
bull Improved QTL estimation when QTLs
bull PROC QTL software
httpstatgenucredudownloadsoftwar
ePROC20QTLpdf
bull Better markers and marker effects for
calculating selection index weights
bull Redoing QTL estimates with new map
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Bayesian vs Interval Mapping 2010 MARS Pilot Project Data Senegal - 100 grain weight
Interval mapping
1 2 3 4 5 6 7 8 9 10 11
LO
D s
core
00
10
20
30
40
50
Bayesian analysis
Chromosome
1 2 3 4 5 6 7 8 9 10 11
Eff
ect
estim
ate
-04
-02
00
02
04
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Activity 4 Capacity Building
bull Two PhD students
Senegal (Penda Sarr - English at UCR Spring 2010 now
enrolled at Anta Diop Chiekh University Dakar Senegal)
Mozambique (Arsenio Ndeve - English at UCR Spring 2010
accepted for Winter 2012 enrollment at UCR)
MABC and MARS breeding
bull PhD student at WACCI (started Sept 2009)
Burkina Faso (Joseph Batieno)
Supported by GCP Capacity Building funds
bull Mentoring
Rogerio Chiulele (Mozambique ndash PhD completed ACCI May
2011)
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Mentoring WACCI PhDs
bull WACCI Cowpea PhD students
ndash Joseph Batieno ndash INERA-Burkina Faso PhD started 2009
ndash Maureen Nkoumki ndashIRAD-Cameroon PhD started 2010
ndash Mohamad Lawan ndash IAR-Nigeria PhD started 2010
ndash Fafa Egbadzor ndash Univ of Ghana PhD started 2010
bull Presented Breeding Training Module March 21 ndash 25
2011 at WACCI
bull Reviewing WACCI Student PhD Proposals
bull Assisting with GCP-GSS Proposal Development
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile
Thank You University of California Riverside
Muchero Wellington
Pottorff Marti
Wanamaker Steve
Ehlers Jeffrey D
Roberts Philip A
Close Timothy J
Lucas Mitchell
Xu Shizhong
Hu Zhiqui
19
National Agricultural Research System (NARS)
Cisse Ndiaga ISRA-Senegal
Drabo Issa INERA-Burkina Faso
Tignegre Jean-Baptist INERA Burkina Faso
Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA)
Muranaka Satoru
Boukar Ousmane
Fatokun Christian
Franco Jorge
Sam Ofodile