grm 2013: improve cowpea productivity for marginal environments in sub-saharan africa -- p roberts
DESCRIPTION
TRANSCRIPT
Tropical Legumes 1 Objective 2
Improve cowpea productivity for marginal environments in sub-Saharan Africa
Phil Roberts Tim Close Bao Lam Huynh ndash UC Riverside Ndiaga Cisse Penda Sarr - ISRA Senegal Issa Drabo Jean-Baptiste Tignegre - INERA Burkina Faso Rogerio Chiulele Arsenio Ndeve - E Mondlane U Mozambique Ousmane Boukar Sam Ofodile Christian Fatokun - IITA Nigeria
GCP General Research Meeting Lisbon September 2013
TL1 Phase II (June 2010 ndash present)
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
G3 300 4-way x 4-way intercrosses yielding 8-way F1s Fall 2011
G2 ~330 pair crosses made Spring 2011
Activity 1 Product MAGIC population
G4 Single seed descent of F2s 2012-2013
o Most now at F5 ndash F6 seed o Planted now to produce F6 amp F7
2-ways amp 8-ways SNP-validated 2012-2013
Activity 2 Products Genomic resources in support of marker-assisted breeding
a Improved consensus map
b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions (eg SNP selection)
c Sets of markers were selected and data produced for MARS and MABC
d QTL discovered in 3 of 5 MARS populations - ICI Mapping (IBP tool)
e Breeding values amp selection indices developed for MARS individuals for intermating ndash OptiMAS (IBP tool)
f QTL for heat tolerance and aphid resistance discovered in elite populations
2a Improved Consensus Map (v6)
bull 11 RIL populations
bull rogues removed
bull 1117 genotyped
bull 1091 mapped SNPs
bull 816 bins
bull improved order
bull clarified synteny with other legumes
Latest version (v6) available on wwwHarvESTCowpea Last published version (v4) is in Lucas et al 2011 Cowpea (Vu) and common
bean (Pv) synteny
Genotyping ICI Mapping
OptiMAS Selection Crossing Planting
New genotyping
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
1 2 3
4
5 6 7
8
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
bull Interacted with the GCP GSS (He Delannay) GDMS (McLaren Ereful Trushar) and KBioscience (GLC) to streamline sample organization and data flow
bull Extensive use of GLC genotyping for MARS and MABC has led to improvements in standard operating procedure
ndash Established an inventory of sample collection plates at each breeder location
ndash Matched positions of samples in plates with field plot maps
ndash Increased all dialog to improve flow of leaf samples to GLC for genotyping
ndash Improved data interpretation and application to MARS amp MABC
Activity 3 Products Employ MARS amp MABC QTL Discovery
a MARS populations for Burkina Faso Mozambique Nigeria and Senegal genotyped and phenotyped
b Continued MABC to develop improved breeding lines ndash genotyping amp phenotyping
c Implemented MAB tools (OptiMAS ICI mapping) training on beta versions of Fieldbook
d QTL for heat tolerance and aphid resistance discovered in elite populations
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
TL1 Phase II (June 2010 ndash present)
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
G3 300 4-way x 4-way intercrosses yielding 8-way F1s Fall 2011
G2 ~330 pair crosses made Spring 2011
Activity 1 Product MAGIC population
G4 Single seed descent of F2s 2012-2013
o Most now at F5 ndash F6 seed o Planted now to produce F6 amp F7
2-ways amp 8-ways SNP-validated 2012-2013
Activity 2 Products Genomic resources in support of marker-assisted breeding
a Improved consensus map
b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions (eg SNP selection)
c Sets of markers were selected and data produced for MARS and MABC
d QTL discovered in 3 of 5 MARS populations - ICI Mapping (IBP tool)
e Breeding values amp selection indices developed for MARS individuals for intermating ndash OptiMAS (IBP tool)
f QTL for heat tolerance and aphid resistance discovered in elite populations
2a Improved Consensus Map (v6)
bull 11 RIL populations
bull rogues removed
bull 1117 genotyped
bull 1091 mapped SNPs
bull 816 bins
bull improved order
bull clarified synteny with other legumes
Latest version (v6) available on wwwHarvESTCowpea Last published version (v4) is in Lucas et al 2011 Cowpea (Vu) and common
bean (Pv) synteny
Genotyping ICI Mapping
OptiMAS Selection Crossing Planting
New genotyping
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
1 2 3
4
5 6 7
8
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
bull Interacted with the GCP GSS (He Delannay) GDMS (McLaren Ereful Trushar) and KBioscience (GLC) to streamline sample organization and data flow
bull Extensive use of GLC genotyping for MARS and MABC has led to improvements in standard operating procedure
ndash Established an inventory of sample collection plates at each breeder location
ndash Matched positions of samples in plates with field plot maps
ndash Increased all dialog to improve flow of leaf samples to GLC for genotyping
ndash Improved data interpretation and application to MARS amp MABC
Activity 3 Products Employ MARS amp MABC QTL Discovery
a MARS populations for Burkina Faso Mozambique Nigeria and Senegal genotyped and phenotyped
b Continued MABC to develop improved breeding lines ndash genotyping amp phenotyping
c Implemented MAB tools (OptiMAS ICI mapping) training on beta versions of Fieldbook
d QTL for heat tolerance and aphid resistance discovered in elite populations
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
G3 300 4-way x 4-way intercrosses yielding 8-way F1s Fall 2011
G2 ~330 pair crosses made Spring 2011
Activity 1 Product MAGIC population
G4 Single seed descent of F2s 2012-2013
o Most now at F5 ndash F6 seed o Planted now to produce F6 amp F7
2-ways amp 8-ways SNP-validated 2012-2013
Activity 2 Products Genomic resources in support of marker-assisted breeding
a Improved consensus map
b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions (eg SNP selection)
c Sets of markers were selected and data produced for MARS and MABC
d QTL discovered in 3 of 5 MARS populations - ICI Mapping (IBP tool)
e Breeding values amp selection indices developed for MARS individuals for intermating ndash OptiMAS (IBP tool)
f QTL for heat tolerance and aphid resistance discovered in elite populations
2a Improved Consensus Map (v6)
bull 11 RIL populations
bull rogues removed
bull 1117 genotyped
bull 1091 mapped SNPs
bull 816 bins
bull improved order
bull clarified synteny with other legumes
Latest version (v6) available on wwwHarvESTCowpea Last published version (v4) is in Lucas et al 2011 Cowpea (Vu) and common
bean (Pv) synteny
Genotyping ICI Mapping
OptiMAS Selection Crossing Planting
New genotyping
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
1 2 3
4
5 6 7
8
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
bull Interacted with the GCP GSS (He Delannay) GDMS (McLaren Ereful Trushar) and KBioscience (GLC) to streamline sample organization and data flow
bull Extensive use of GLC genotyping for MARS and MABC has led to improvements in standard operating procedure
ndash Established an inventory of sample collection plates at each breeder location
ndash Matched positions of samples in plates with field plot maps
ndash Increased all dialog to improve flow of leaf samples to GLC for genotyping
ndash Improved data interpretation and application to MARS amp MABC
Activity 3 Products Employ MARS amp MABC QTL Discovery
a MARS populations for Burkina Faso Mozambique Nigeria and Senegal genotyped and phenotyped
b Continued MABC to develop improved breeding lines ndash genotyping amp phenotyping
c Implemented MAB tools (OptiMAS ICI mapping) training on beta versions of Fieldbook
d QTL for heat tolerance and aphid resistance discovered in elite populations
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Activity 2 Products Genomic resources in support of marker-assisted breeding
a Improved consensus map
b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions (eg SNP selection)
c Sets of markers were selected and data produced for MARS and MABC
d QTL discovered in 3 of 5 MARS populations - ICI Mapping (IBP tool)
e Breeding values amp selection indices developed for MARS individuals for intermating ndash OptiMAS (IBP tool)
f QTL for heat tolerance and aphid resistance discovered in elite populations
2a Improved Consensus Map (v6)
bull 11 RIL populations
bull rogues removed
bull 1117 genotyped
bull 1091 mapped SNPs
bull 816 bins
bull improved order
bull clarified synteny with other legumes
Latest version (v6) available on wwwHarvESTCowpea Last published version (v4) is in Lucas et al 2011 Cowpea (Vu) and common
bean (Pv) synteny
Genotyping ICI Mapping
OptiMAS Selection Crossing Planting
New genotyping
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
1 2 3
4
5 6 7
8
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
bull Interacted with the GCP GSS (He Delannay) GDMS (McLaren Ereful Trushar) and KBioscience (GLC) to streamline sample organization and data flow
bull Extensive use of GLC genotyping for MARS and MABC has led to improvements in standard operating procedure
ndash Established an inventory of sample collection plates at each breeder location
ndash Matched positions of samples in plates with field plot maps
ndash Increased all dialog to improve flow of leaf samples to GLC for genotyping
ndash Improved data interpretation and application to MARS amp MABC
Activity 3 Products Employ MARS amp MABC QTL Discovery
a MARS populations for Burkina Faso Mozambique Nigeria and Senegal genotyped and phenotyped
b Continued MABC to develop improved breeding lines ndash genotyping amp phenotyping
c Implemented MAB tools (OptiMAS ICI mapping) training on beta versions of Fieldbook
d QTL for heat tolerance and aphid resistance discovered in elite populations
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
2a Improved Consensus Map (v6)
bull 11 RIL populations
bull rogues removed
bull 1117 genotyped
bull 1091 mapped SNPs
bull 816 bins
bull improved order
bull clarified synteny with other legumes
Latest version (v6) available on wwwHarvESTCowpea Last published version (v4) is in Lucas et al 2011 Cowpea (Vu) and common
bean (Pv) synteny
Genotyping ICI Mapping
OptiMAS Selection Crossing Planting
New genotyping
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
1 2 3
4
5 6 7
8
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
bull Interacted with the GCP GSS (He Delannay) GDMS (McLaren Ereful Trushar) and KBioscience (GLC) to streamline sample organization and data flow
bull Extensive use of GLC genotyping for MARS and MABC has led to improvements in standard operating procedure
ndash Established an inventory of sample collection plates at each breeder location
ndash Matched positions of samples in plates with field plot maps
ndash Increased all dialog to improve flow of leaf samples to GLC for genotyping
ndash Improved data interpretation and application to MARS amp MABC
Activity 3 Products Employ MARS amp MABC QTL Discovery
a MARS populations for Burkina Faso Mozambique Nigeria and Senegal genotyped and phenotyped
b Continued MABC to develop improved breeding lines ndash genotyping amp phenotyping
c Implemented MAB tools (OptiMAS ICI mapping) training on beta versions of Fieldbook
d QTL for heat tolerance and aphid resistance discovered in elite populations
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Genotyping ICI Mapping
OptiMAS Selection Crossing Planting
New genotyping
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
1 2 3
4
5 6 7
8
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
bull Interacted with the GCP GSS (He Delannay) GDMS (McLaren Ereful Trushar) and KBioscience (GLC) to streamline sample organization and data flow
bull Extensive use of GLC genotyping for MARS and MABC has led to improvements in standard operating procedure
ndash Established an inventory of sample collection plates at each breeder location
ndash Matched positions of samples in plates with field plot maps
ndash Increased all dialog to improve flow of leaf samples to GLC for genotyping
ndash Improved data interpretation and application to MARS amp MABC
Activity 3 Products Employ MARS amp MABC QTL Discovery
a MARS populations for Burkina Faso Mozambique Nigeria and Senegal genotyped and phenotyped
b Continued MABC to develop improved breeding lines ndash genotyping amp phenotyping
c Implemented MAB tools (OptiMAS ICI mapping) training on beta versions of Fieldbook
d QTL for heat tolerance and aphid resistance discovered in elite populations
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
bull Interacted with the GCP GSS (He Delannay) GDMS (McLaren Ereful Trushar) and KBioscience (GLC) to streamline sample organization and data flow
bull Extensive use of GLC genotyping for MARS and MABC has led to improvements in standard operating procedure
ndash Established an inventory of sample collection plates at each breeder location
ndash Matched positions of samples in plates with field plot maps
ndash Increased all dialog to improve flow of leaf samples to GLC for genotyping
ndash Improved data interpretation and application to MARS amp MABC
Activity 3 Products Employ MARS amp MABC QTL Discovery
a MARS populations for Burkina Faso Mozambique Nigeria and Senegal genotyped and phenotyped
b Continued MABC to develop improved breeding lines ndash genotyping amp phenotyping
c Implemented MAB tools (OptiMAS ICI mapping) training on beta versions of Fieldbook
d QTL for heat tolerance and aphid resistance discovered in elite populations
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Activity 3 Products Employ MARS amp MABC QTL Discovery
a MARS populations for Burkina Faso Mozambique Nigeria and Senegal genotyped and phenotyped
b Continued MABC to develop improved breeding lines ndash genotyping amp phenotyping
c Implemented MAB tools (OptiMAS ICI mapping) training on beta versions of Fieldbook
d QTL for heat tolerance and aphid resistance discovered in elite populations
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Institution Population SNPs Current Stage
INERA Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross
IITA Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1
102 95
Cycle 1 Intercross Terminated
EMU Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross
ISRA Senegal IT93K-503-1 x Mouride 136 Adjusted Now F2F6
3a MARS Breeding Progress
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Phenotyping Basis of MARS QTL Discovery ndash 2011 amp 2012
Nigeria - Ousmane Boukar
Mozambique ndash Rogerio Chiulele
Senegal ndash Ndiaga Cisse
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Example Traits measured in 250 F23 families at two field sites
in Burkina Faso Issa Drabo
Set2 Traits 140 lines lt100 seedsline
Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weightplot Seed weightplot 100-seed weight
Set1 110 lines gt=100 seedsline
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
0 100 200 300 400 500 600 700 800
Position in the whole genome
0
1
2
3
4
5
6
7
8
9
LO
D S
core
QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
QTL effects on yield and seed weight Yield-8 (1_0033)
A Suvita-2 allele B IT97K-499-35 allele
0
50
100
150
200
250
300Se
ed w
eigh
t per
plo
t (g)
AA
AB
BB
10
12
14
16
18
20
22
100-
seed
wei
ght (
g)
AA
AB
BB
GDW-11 (1_0771)
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Genotyping plants derived from intercrossing of F24 individuals
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Take-home message clear acceleration toward ideotypes
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Selected best families using OptiMAS
StrigaYLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
243 083 100 050 050 100 100 100 Yes71 083 100 100 050 100 050 100 Yes281 079 100 050 098 050 100 073 Yes51 075 100 050 100 100 050 050 Yes190 075 050 100 098 050 100 050 Yes154 071 050 100 100 050 050 073 Yes112 042 100 050 050 050 000 000 No235 042 050 000 050 050 050 050 No251 042 050 000 050 050 050 050 No199 019 062 000 000 000 050 000 No285 017 000 000 050 000 000 050 No99 017 000 000 000 000 000 100 No
SelectedF23 family
Molecular score
Yield QTLs Kernel-size QTLs
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Frequency of favorable alleles at different selection steps (on average and for each QTL)
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Activity 3b Employ MABC to develop improved breeding lines
bull 11 populations in progress (2 Jean-BaptisteIssa 2 Rogerio 1 Ndiaga 3 Boukar 3 UCR)
bull Identified all polymorphic markers from SNP database
bull Selected trait markers and background markers at 2 cM intervals
bull Genotypedphenotyped different generations BC1F1 BC1F2 BC1F6 BC2F1 BC2F4 BC3F4
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Activity 3b Employ MABC to develop improved breeding lines
Program Cross Main Donor Traits
INERA MoussaIT93K-693-2Moussa KVX745-11PKVX414-22KVX745-11P
Striga Striga Seed Size
IITA IT93K-452-1IT97K-499-35IT93K-452-1 IT89KD-288IT97K-499-35IT89KD-288 SuVita 2IT97K-499-35SuVita 2
Striga Striga Drought Striga
EMU CB27IT85F-3139IT85F-3139 CB27INIA-41CB27
Grain Quality Nematode Drought
ISRA MelakhIT97K-499-39Melakh Striga
UCR CB27IT97K-556-6CB27 CB46IT97K-556-6CB46 CB50IT97K-556-6CB50
Aphid Aphid Aphid
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Genetic map and trait-linked markers 1_0972
1_1278
1_09501_01291_00551_0100
1_1088
1_0647
1_08761_0034
1_1177
1_04491_15261_00721_12751_00851_07821_13761_07491_03081_05401_13571_07751_00631_03331_07901_11511_01301_07341_01501_08371_11111_14681_0319
Aphid1_09281_13441_04151_02801_06301_15341_00591_03121_05321_14041_07261_03831_03961_0640
1_1424
1_07251_02381_0645
1_08171_0365
1_06251_02561_06141_07841_0855
1_03441_04401_11561_04351_14201_1193
1_00751_00121_1152
1_0748
1_0320
1_0811
Drought
LG11_11291_13641_01841_02031_02681_0657
1_1371
1_02951_1067
1_0113
1_1523
1_12581_00211_07921_00891_14691_08441_0277
Yield1_06981_08291_04921_02531_03371_01641_01691_13721_10861_00611_04531_02841_14061_11391_05251_05851_10611_10481_15051_09341_02191_02641_07161_10591_1096
Heat1_01701_05341_11581_09931_00621_02151_06871_14491_11661_11811_04811_06931_11401_11491_02081_09941_14311_07211_13921_11571_05951_07411_04821_07911_14901_10331_01441_03281_02401_09851_00411_14701_15351_12301_11081_02111_06701_06741_02291_00091_13521_06331_06521_06951_11541_04301_14471_06581_13991_10391_01951_01511_07531_06791_05121_01151_02851_04981_11151_12341_05511_08851_07731_06941_12351_14321_01031_02371_12621_13781_03171_10631_01601_07091_14561_13791_05131_08151_10211_10931_14811_01381_06111_15271_06421_14951_02971_04991_08491_10061_11051_04051_08341_04891_05991_0445
LG21_07641_00711_01831_04581_06831_00801_04831_04471_01461_0147
Mac1_07241_10371_13511_07791_01851_00701_02041_06671_09371_12061_05911_02321_00571_09421_11951_00311_02441_05461_04291_15121_10721_14551_10561_1416
Staygreen1_02171_11171_04591_05091_04241_14831_00871_01041_03481_12401_04651_00171_04751_01161_05711_11451_04431_13961_00201_00681_01331_01541_13491_06361_10241_01781_07611_13501_15251_05111_07131_10231_12221_0788
Nematode1_12931_12241_07581_10221_14271_00861_12861_00641_12051_13581_05451_13481_02991_06861_11711_09821_01451_12771_11221_07401_02431_10051_01631_01761_14391_02471_09711_13001_09591_09681_06541_04001_09531_04441_10271_01391_02071_13691_09381_06041_08311_10751_11091_10851_10871_03521_02651_09841_03801_1162
1_05941_03881_11341_03451_07181_14521_09641_03311_10151_15131_04041_09001_02091_07691_15221_0812
Biomass1_0491
1_08201_07721_10791_08931_03811_01941_10581_11061_06191_12921_11211_0707
Heat1_02011_06181_04641_15001_01971_12311_01211_01361_00931_07761_12411_09901_03731_10281_05691_09211_06811_06011_14121_12871_09511_01021_08821_02361_08781_05931_11161_01051_10471_03031_03011_06561_13751_06261_09891_0234
Mac1_12511_01991_09461_01801_10731_12991_10651_11441_01431_04361_01751_06551_0539
LG31_03641_0052
Yield1_00541_08541_01881_03421_04561_08031_09731_10321_11471_05041_03821_11481_03971_09691_03141_03211_09761_06731_06721_08901_01901_05721_05021_13601_14991_05801_11381_10341_01551_00821_07561_14451_08471_07741_12211_12421_00271_01531_12611_05351_10921_06461_08741_08261_06921_04031_0106
1_06781_1209
1_01171_0128
1_13161_0157
1_00381_09101_10131_0992
1_00831_04171_0349
1_03981_08561_0543
1_0699
1_08041_0275
1_03041_02001_07461_01221_02671_04071_05081_08751_11461_13191_1191
LG41_10031_00451_0684
Yield1_03091_11321_04421_13661_1232
1_0605
1_00951_03351_08061_02921_07891_02711_05071_0979
1_1001
1_04781_0624
1_01731_0819
1_0452
1_0557
1_1492
1_01911_02731_0510
1_06621_0986
1_00301_0872
1_0800
1_00401_03621_08771_04191_05781_13591_09261_02421_08391_14191_01191_12531_12431_1095
1_02511_03461_06771_15331_02051_00811_02251_03991_01271_13221_00321_01931_02871_11281_01201_09451_06611_08661_02261_00371_08791_09241_05481_04951_09981_05881_03791_00991_08891_09351_05791_02311_03871_09741_14011_01651_00041_09231_11721_00781_11651_15071_03741_11301_0733
LG51_0962
1_03231_06911_03071_01721_01741_13331_13681_03001_06351_06901_07511_09081_09271_13311_15301_00241_08231_14031_00661_15151_12261_10971_04321_00741_07321_03321_04851_00841_08251_10821_04541_02161_03691_09191_14961_01861_06881_06751_0939
1_02241_08711_13431_09111_08301_06601_13811_08951_10771_13631_08971_08601_14841_11071_07041_05441_14431_01481_02901_10201_07011_00261_10901_0538
1_07941_01241_12441_1080
1_07601_1194
Heat1_13671_04371_12981_00151_06641_09431_00181_10121_0706
1_06391_0975
1_10421_05221_0880
1_01231_05411_10431_00101_03471_0765
1_00141_07361_12711_05421_0326
1_0514
1_09331_04261_03671_01711_14861_15081_06501_12731_0947
1_1007
LG6Heat1_0881
1_15211_02611_07631_14181_10141_00061_12661_14461_0719
1_01981_11411_1302
1_07111_15361_05291_04391_02781_07231_01261_0047
Yield1_06311_12151_10261_03851_06591_15101_1414
Drought1_05611_05641_0644
Staygreen1_14821_01681_00231_03841_09061_09121_14721_07551_0196
Aphid1_07081_06631_10571_04771_10351_06481_06961_09171_02281_06411_02701_08841_11861_06211_03921_10601_00191_04691_06321_08831_13151_08641_11131_02941_05761_05591_08241_00561_03051_09441_12491_14651_00391_02481_00161_1135
LG71_0519
1_13411_0842
1_08581_0298
1_0022
1_13701_0302
1_05581_13621_03941_08131_1008
1_04511_0771
1_0567
1_01411_04101_07621_01311_03511_09181_11851_13611_08071_11681_11231_06651_12841_00441_05241_06491_07971_02551_12601_10991_00761_06431_11011_08011_08921_05301_04381_0616
1_1218
1_0353
1_0838
1_0306
1_1374
1_09571_05861_05661_0832
1_1199
1_01871_0250
1_12521_0375
1_1246
1_0750
1_0241
1_09671_00581_15291_11981_04021_13931_11691_01671_02331_0324
LG81_02131_12021_10161_11671_00881_06681_0720
1_07121_1347
Nematode1_04871_09491_09651_12081_02461_08671_07951_08571_03771_03891_09991_12361_07281_00971_06511_09871_04481_02211_11591_06341_10381_00511_01011_01121_00901_03381_00011_14911_00351_05001_11921_12911_00481_03711_02661_00251_04801_05651_1217
1_01791_0259
1_1408
1_0421
1_00081_04731_02351_13821_14601_01581_01371_11881_04311_07521_03581_02141_02541_1467
1_0425
1_02571_12551_0474
1_13371_02761_0958
1_07031_09481_10691_1045
LG91_03561_10891_14091_14071_09771_11201_1118
1_11891_02881_04931_0036
1_0401
1_10811_12541_03301_15091_14781_1225
1_01111_11261_0109
1_00021_03291_10171_14021_00771_07801_1098
1_0341
1_04161_10491_15201_09811_08651_10761_14441_10251_05871_0628
Yield1_00501_0598
Drought1_05011_10181_08331_0739
Staygreen1_00651_07541_05371_09301_02811_05541_13561_14531_03541_04571_00531_02491_07301_09521_10621_01611_10411_00031_04061_05831_14301_09601_00071_12811_0060
1_1263
1_04201_08511_03681_04461_02301_02821_06821_01421_08611_10941_14341_01071_06171_08621_0239
LG101_0940
1_08861_07021_1052
1_0603
1_0905
1_0134
1_05311_08051_08941_1164
1_0125
Nematode1_04141_13901_09701_0961
1_0028
1_0802
1_11241_00331_12231_07221_03391_05631_12371_13881_08181_09961_00431_00961_01101_05501_12141_13981_06001_05741_02121_08591_09541_13451_13271_04861_09661_03111_11031_09321_04941_02741_06371_09551_10041_00131_06081_14401_11371_05621_06661_05061_11971_0322
1_0547
1_0629
1_0606
1_0069
1_1377
1_04221_08161_1180
1_0553
1_0787
1_1417
LG110
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
3 Products QTL identified for multiple traits
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
CB27 (tolerant) x IT82E-18 (sensitive)
Tolerant RIL Sensitive RIL
3d Heat Tolerance QTL in Elite RILs
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Map positions of five heat tolerance QTL
Cht-1 Cht-2
Cht-3
Cht-4
Cht-5
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
CB27 (sensitive) x IT97K-556-6 (resistant)
S R
3d Aphid Resistance QTL in Elite RILs
S
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
QTLs for aphid resistance in CB27 x IT97K-556-6
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11
Major QTL 66
phenotypic variance
Minor QTL 9 phenotypic
variance
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Activity 4 Products Capacity Building
Two PhD students bull Senegal (Penda Sarr ndash enrolled 2011 at Anta Diop Chiekh
University Dakar Senegal)
bull Mozambique (Arsenio Ndeve ndash enrolled Winter 2012 at UCR)
bull Jointly supported by GCP and USAID CRSP bull MABC and MARS breeding
PhD students at WACCI bull Burkina Faso (Joseph Batieno) ndash MABC project
supported by GCP Capacity Building funds bull Ken Fafa ndash using KBio SNPs for cowpea seed size
MSc students at E Mondlane U Mozambique bull Mentoring in plant breeding with Rogerio Chiulele
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Activity 5 Products Data Curation amp Storage
bull TL-1 datasets ndash Provided genotype datasets to GCP curators (Trushar)
bull 1536-SNP Illumina platform bull ~650 germplasm accessions bull Includes almost all MARS and MABC parents
ndash Organized phenotype datasets UCR in collaboration with Sam Ofodile at IITA
bull uniform naming conventions file structure error detection bull 34 cowpea phenotyping datasets standardized at UCR (I
Flores) and sent to IITA (S Ofodile)
ndash Added historical pedigrees of IITA lines amp pedigrees of TL-1 materials to IITAGCP database
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Thank You University of California Riverside Roberts Philip A Close Timothy J Huynh Bao Lam Lucas Mitchell Ndeve Arsenio Pottorff Marti Wanamaker Steve Xu Shizhong Hu Zhiqui
26
National Agricultural Research System (NARS) Cisse Ndiaga ISRA-Senegal Drabo Issa INERA-Burkina Faso Tignegre Jean-Baptiste INERA Burkina Faso Rogerio Chiulele Eduardo Mondlane U Mozambique
International Institute of Tropical Agriculture (IITA) Boukar Ousmane Fatokun Christian Ofodile Sam
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Validation of MAGIC population by SNP genotyping Method
Identified 91 parent-unique SNPs KBio genotyping
Results 2-ways (91 SNPs)
Number of crosses tested ndash All - 72 Number of crosses validated ndash all (100)
8-ways (78 SNPs) Assayed for presence of all four 2-ways in parentage Number of crosses genotyped - 368 Validation not yet complete (238 done 126 in progress)
Activity 1 MAGIC population
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Plant Cycle 1_0853 1_0447 1_0146 1_0937 1_00312010-057-190 F2 GG GG AA GG GG2010-057-190-01 F4 GG GG AA GG GG2010-057-190-02 F4 GG -- AA -- GG2010-057-190-03 F4 GG GG AA GG GG2010-057-190-04 F4 GG GG AA GG GG2010-057-190-05 F4 GA GC GA GC GA2010-057-190-06 F4 GG GG AA GG GG2010-057-190-07 F4 GG GG AA GG GG2010-057-190-08 F4 GG GG AA GG GG2010-057-190-09 F4 GG GG AA GG GG2010-057-190-10 F4 GA GC GA GC GA
Elimination of Detected Outcrosses
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Heterozygous for donor allele
of the Striga resistance
marker
Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
MARS ndash Burkina Genotyping 10 individuals of each selected family
Yield-8 (1_0033) GDW-11 (1_0771)
Favorable allele
Favorable allele
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Background and QTL selection within BC1F1
Striga1_0298 1_0022 1_1370 1_0451 1_0567 1_0583
Moussa (recurrent) 100 AA AA AA AA AA AAIT97K-499-35 (donor) 0 BB BB BB BB BB BBF1 50 AB AB AB AB AB ABM499_BC1F1_12 92 AA AA AA AA AA AAM499_BC1F1_25 88 AA AA AA AA AA AAM499_BC1F1_43 86 AB AB AB AB AB AAM499_BC1F1_04 85 AB AB AB AB AB AB YesM499_BC1F1_06 81 AA AA AA AA AA ABM499_BC1F1_35 80 AA AA AA AA AA AAM499_BC1F1_20 80 AB AB AB AB AB AAM499_BC1F1_21 78 AA AA AA AA AA ABM499_BC1F1_29 77 AA AA AA AA AA AAM499_BC1F1_10 75 AB AB AB AB AB AB YesM499_BC1F1_01 75 AA AA AA AA AA AAM499_BC1F1_73 67 AA AA AA AA AA ABM499_BC1F1_67 64 AB AB AB AB AB ABM499_BC1F1_28 64 AA AB AA AB AB ABM499_BC1F1_16 61 AB AB AB AB AB AB
Plant ID Moussa Selected for BC2
Yield
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
BC2F1 plants (Leaf samples submitted to KBiosciences Possible BC3 crosses being
made while awaiting genotypic data)
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
3d QTL Discovery in Elite RILs
Heat Tolerance ndash CB27 x IT82E-18 ndash Yield yield components ndash Phenotyped Summers 2010 amp 2011 ndash QTL analysis in 2012 ndash 5 QTL discovered ndash Lucas et al 2012 Markers for
Breeding Heat Tolerant Cowpea Molecular Breeding 31529-536
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Other Cross-Cutting Physiological Trait QTL Mapping
bull Water deficit bull Vincent Vadez ICRISAT
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
3d Aphid Resistance QTL in Elite RILs Aphid Resistance
ndash CB27 x IT97K-556-6 ndash Phenotyped in Summer 2010 2011 amp
2012 in California bull Weak aphid pressure 2010 amp 2011 bull Heavy aphid pressure in 2012
ndash QTL analysis ndash very distinct QTL in 2012
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Selected best individuals using OptiMAS
Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
71 F2 083 100 100 050 100 050 100
71-03 F4 092 100 100 050 100 100 100 Yes
71-02 F4 092 100 100 100 100 050 100 Yes
71-10 F4 092 100 100 100 100 050 100 Yes
71-01 F4 075 100 100 052 100 000 100 No
71-04 F4 075 100 100 000 100 050 100 No
71-05 F4 075 100 100 050 100 000 100 No
71-07 F4 067 100 100 000 100 000 100 No
SelectedPlant ID Cycle MS Yield QTLs Kernel-size QTLs
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-
Linkages with TL-2 Project Genotyping and Analyses for TL-2
bull 201112 ndash SNP-genotyped 321 TL-2 lines that looked promising in multiple TL-2 drought trials
bull association analysis phenotype-genotype bull no significant QTLs observed
Identified top priorities for marker validation in TL-2 materials ndash Hyderabad October 2012
bull Bacterial blight resistance bull Thrips resistance bull Aphid resistance bull Now working on MABC ndash common populations
- Slide Number 1
- TL1 Phase II (June 2010 ndash present)
- Activity 1 Product MAGIC population
- Activity 2 Products Genomic resources in support of marker-assisted breeding
- Slide Number 5
- Slide Number 6
- 2b Refined the GCP cowpea genotyping workflow and supported GSS-client interactions
- Activity 3 Products Employ MARS amp MABC QTL Discovery
- Slide Number 9
- Slide Number 10
- Example Traits measured in 250 F23 families at two field sites in Burkina Faso Issa Drabo
- QTLs from ICI Mapping ndash Burkina Faso Issa Drabo
- QTL effects on yield and seed weight
- Genotyping plants derived from intercrossing of F24 individuals
- Slide Number 15
- Slide Number 16
- Slide Number 17
- Slide Number 18
- Genetic map and trait-linked markers
- 3d Heat Tolerance QTL in Elite RILs
- Slide Number 21
- CB27 (sensitive) x IT97K-556-6 (resistant)
- QTLs for aphid resistance in CB27 x IT97K-556-6
- Activity 4 Products Capacity Building
- Activity 5 Products Data Curation amp Storage
- Thank You
- Slide Number 27
- Activity 1 MAGIC population
- Slide Number 29
- Genotyping BC1F1 of Moussa x IT97K-499-35 (donor)
- MARS ndash Burkina Genotyping 10 individuals of each selected family
- Background and QTL selection within BC1F1
- BC2F1 plants(Leaf samples submitted to KBiosciences Possible BC3 crosses being made while awaiting genotypic data)
- 3d QTL Discovery in Elite RILs
- Other Cross-Cutting
- 3d Aphid Resistance QTL in Elite RILs
- Slide Number 37
- Linkages with TL-2 Project
-