TLM III: Improve cowpea productivity for marginal environments in sub-Saharan Africa – O Boukar
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This document summarizes activities from Phase II of the Tropical Legumes 1 project, which aims to improve cowpea productivity in marginal environments in sub-Saharan Africa. Key activities included developing a multi-parent advanced generation intercross (MAGIC) population, generating genomic resources like an improved consensus map, and employing marker-assisted recurrent selection (MARS) and marker-assisted backcrossing (MABC) to develop improved cowpea lines. The project involved multiple institutions across Africa and generated important products like a MAGIC population, genomic resources, quantitative trait loci (QTL) discoveries, and preliminary advanced breeding lines.
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TLM III: Improve cowpea productivity for marginal environments in sub-Saharan Africa – O Boukar
- 1. Tropical Legumes 1: Objective 2 Improve cowpea productivity for marginal environments in sub-Saharan Africa Phil Roberts, Tim Close, Bao Lam Huynh – UC Riverside Ndiaga Cisse, Penda Sarr - ISRA, Senegal Issa Drabo, Jean-Baptiste Tignegre - INERA, Burkina Faso Rogerio Chiulele, Arsenio Ndeve - E. Mondlane U, Mozambique Ousmane Boukar, Sam Ofodile, Christian Fatokun - IITA, Nigeria
- 2. TL1 Phase II (June 2010 – present) • Activity 1: Develop MAGIC population • Activity 2: Develop genomic resources in support of marker-assisted breeding • Activity 3: Employ MARS and MABC to develop improved breeding lines • Activity 4: Capacity Building • Activity 5: Curate and Store Phase I and II Data
- 3. G3: 300 4-way x 4-way intercrosses yielding 8-way F1s; Fall 2011 G2: ~330 pair crosses made, Spring 2011 Activity 1 Product: MAGIC population G4: Single seed descent of F2s 2012- 2013 o Most now at F6 – F7 seed *2-ways & 8-ways SNP-validated 2012-2013
- 4. Activity 2 Products: Genomic resources in support of marker-assisted breeding a. Improved consensus map b. Refined the GCP cowpea genotyping workflow and supported GSS-client interactions (e.g. SNP selection) c. Sets of markers were selected and data produced for MARS and MABC d. QTL discovered in 3 of 5 MARS populations - ICI Mapping (IBP tool) e. Breeding values & selection indices developed for MARS individuals for intermating – OptiMAS (IBP tool) f. QTL for heat tolerance and aphid resistance discovered in elite populations
- 5. 2a. Improved Consensus Map (v6) • 11 RIL populations • rogues removed • 1117 genotyped • 1091 mapped SNPs • 816 bins • improved order • clarified synteny with other legumes Latest version (v6) available on www.HarvEST:Cowpea Last published version (v4) is in Lucas et al. 2011 Cowpea (Vu) and common bean (Pv) synteny
- 6. Genotyping ICI Mapping OptiMAS Selection Crossing Planting New genotyping 2b. Refined the GCP cowpea genotyping workflow and supported GSS-client interactions 1 2 3 4 567 8
- 7. 2b. Refined the GCP cowpea genotyping workflow and supported GSS-client interactions • Interacted with the GCP GSS (He, Delannay), GDMS (McLaren, Ereful, Trushar) and KBioscience (GLC) to streamline sample organization and data flow • Extensive use of GLC genotyping for MARS and MABC has led to improvements in standard operating procedure – Established an inventory of sample collection plates at each breeder location – Matched positions of samples in plates with field plot maps – Increased all dialog to improve flow of leaf samples to GLC for genotyping – Improved data interpretation and application to MARS & MABC
- 8. Activity 3 Products: Employ MARS & MABC; QTL Discovery a. MARS populations for Burkina Faso, Mozambique, Nigeria and Senegal genotyped and phenotyped b. Continued MABC to develop improved breeding lines – genotyping & phenotyping c. Implemented MAB tools (OptiMAS, ICI mapping), training on beta versions of Fieldbook d. QTL for heat tolerance and aphid resistance discovered in elite populations
- 9. Institution Population SNPs Current Stage INERA, Burkina Faso Suvita 2 x IT97K-499-35 164 Cycle 2 Intercross IITA, Nigeria IT84S-2246 x IT98K-1111-1 IT97K-499-35 x IT93K-503-1 102 95 Cycle 1 Intercross Terminated EMU, Mozambique CB27 x IT97K-499-35 156 Cycle 1 Intercross ISRA, Senegal IT93K-503-1 x Mouride 136 Adjusted, Now F2:F6 3a. MARS Breeding Progress
- 10. Phenotyping Basis of MARS QTL Discovery – 2011 & 2012 Nigeria - Ousmane Boukar Mozambique – Rogerio Chiulele Senegal – Ndiaga Cisse
- 11. Example: Traits measured in 250 F2:3 families at two field sites in Burkina Faso; Issa Drabo Set#2 Traits 140 lines, <100 seeds/line Pobe Saria Saria Number of plants Maturity Flowering time Virus symptoms Pod weight/plot Seed weight/plot 100-seed weight Set#1 110 lines, >=100 seeds/line
- 12. 0 100 200 300 400 500 600 700 800 Position in the whole genome 0 1 2 3 4 5 6 7 8 9 LODScore QTLs from ICI Mapping – Burkina Faso, Issa Drabo VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
- 13. Selected best families using OptiMAS Striga YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3 243 0.83 1.00 0.50 0.50 1.00 1.00 1.00 Yes 71 0.83 1.00 1.00 0.50 1.00 0.50 1.00 Yes 281 0.79 1.00 0.50 0.98 0.50 1.00 0.73 Yes 51 0.75 1.00 0.50 1.00 1.00 0.50 0.50 Yes 190 0.75 0.50 1.00 0.98 0.50 1.00 0.50 Yes 154 0.71 0.50 1.00 1.00 0.50 0.50 0.73 Yes 112 0.42 1.00 0.50 0.50 0.50 0.00 0.00 No 235 0.42 0.50 0.00 0.50 0.50 0.50 0.50 No 251 0.42 0.50 0.00 0.50 0.50 0.50 0.50 No 199 0.19 0.62 0.00 0.00 0.00 0.50 0.00 No 285 0.17 0.00 0.00 0.50 0.00 0.00 0.50 No 99 0.17 0.00 0.00 0.00 0.00 0.00 1.00 No Selected F2:3 family Molecular score Yield QTLs Kernel-size QTLs
- 14. Frequency of favorable alleles at different selection steps (on average and for each QTL)
- 15. Activity 3b: Employ MABC to develop improved breeding lines • 11 populations in progress (2 Jean-Baptiste/Issa, 2 Rogerio, 1 Ndiaga, 3 Boukar, 3 UCR) • Identified all polymorphic markers from SNP database • Selected trait markers and background markers at 2 cM intervals • Genotyped/phenotyped different generations: BC1F1, BC1F2, BC1F6, BC2F1, BC2F4, BC3F4
- 16. Activity 3b: Employ MABC to develop improved breeding lines Program Cross Main Donor Traits INERA Moussa/IT93K-693-2//Moussa KVX745-11P/KVX414-22//KVX745-11P Striga Striga, Seed Size IITA IT93K-452-1/IT97K-499-35//IT93K-452-1 IT89KD-288/IT97K-499-35//IT89KD-288 SuVita 2/IT97K-499-35//SuVita 2 Striga Striga Drought, Striga EMU CB27/IT85F-3139//IT85F-3139 CB27/INIA-41//CB27 Grain Quality Nematode, Drought ISRA Melakh/IT97K-499-39//Melakh Striga UCR CB27/IT97K-556-6//CB27 CB46/IT97K-556-6//CB46 CB50/IT97K-556-6//CB50 Aphid Aphid Aphid
- 17. Genetic map and trait-linked markers 1_0972 1_1278 1_0950 1_0129 1_0055 1_0100 1_1088 1_0647 1_0876 1_0034 1_1177 1_0449 1_1526 1_0072 1_1275 1_0085 1_0782 1_1376 1_0749 1_0308 1_0540 1_1357 1_0775 1_0063 1_0333 1_0790 1_1151 1_0130 1_0734 1_0150 1_0837 1_1111 1_1468 1_0319 Aphid1_0928 1_1344 1_0415 1_0280 1_0630 1_1534 1_0059 1_0312 1_0532 1_1404 1_0726 1_0383 1_0396 1_0640 1_1424 1_0725 1_0238 1_0645 1_0817 1_0365 1_0625 1_0256 1_0614 1_0784 1_0855 1_0344 1_0440 1_1156 1_0435 1_1420 1_1193 1_0075 1_0012 1_1152 1_0748 1_0320 1_0811 Drought LG1 1_1129 1_1364 1_0184 1_0203 1_0268 1_0657 1_1371 1_0295 1_1067 1_0113 1_1523 1_1258 1_0021 1_0792 1_0089 1_1469 1_0844 1_0277 Yield1_0698 1_0829 1_0492 1_0253 1_0337 1_0164 1_0169 1_1372 1_1086 1_0061 1_0453 1_0284 1_1406 1_1139 1_0525 1_0585 1_1061 1_1048 1_1505 1_0934 1_0219 1_0264 1_0716 1_1059 1_1096 Heat1_0170 1_0534 1_1158 1_0993 1_0062 1_0215 1_0687 1_1449 1_1166 1_1181 1_0481 1_0693 1_1140 1_1149 1_0208 1_0994 1_1431 1_0721 1_1392 1_1157 1_0595 1_0741 1_0482 1_0791 1_1490 1_1033 1_0144 1_0328 1_0240 1_0985 1_0041 1_1470 1_1535 1_1230 1_1108 1_0211 1_0670 1_0674 1_0229 1_0009 1_1352 1_0633 1_0652 1_0695 1_1154 1_0430 1_1447 1_0658 1_1399 1_1039 1_0195 1_0151 1_0753 1_0679 1_0512 1_0115 1_0285 1_0498 1_1115 1_1234 1_0551 1_0885 1_0773 1_0694 1_1235 1_1432 1_0103 1_0237 1_1262 1_1378 1_0317 1_1063 1_0160 1_0709 1_1456 1_1379 1_0513 1_0815 1_1021 1_1093 1_1481 1_0138 1_0611 1_1527 1_0642 1_1495 1_0297 1_0499 1_0849 1_1006 1_1105 1_0405 1_0834 1_0489 1_0599 1_0445 LG2 1_0764 1_0071 1_0183 1_0458 1_0683 1_0080 1_0483 1_0447 1_0146 1_0147 Mac1_0724 1_1037 1_1351 1_0779 1_0185 1_0070 1_0204 1_0667 1_0937 1_1206 1_0591 1_0232 1_0057 1_0942 1_1195 1_0031 1_0244 1_0546 1_0429 1_1512 1_1072 1_1455 1_1056 1_1416 Staygreen1_0217 1_1117 1_0459 1_0509 1_0424 1_1483 1_0087 1_0104 1_0348 1_1240 1_0465 1_0017 1_0475 1_0116 1_0571 1_1145 1_0443 1_1396 1_0020 1_0068 1_0133 1_0154 1_1349 1_0636 1_1024 1_0178 1_0761 1_1350 1_1525 1_0511 1_0713 1_1023 1_1222 1_0788 Nematode1_1293 1_1224 1_0758 1_1022 1_1427 1_0086 1_1286 1_0064 1_1205 1_1358 1_0545 1_1348 1_0299 1_0686 1_1171 1_0982 1_0145 1_1277 1_1122 1_0740 1_0243 1_1005 1_0163 1_0176 1_1439 1_0247 1_0971 1_1300 1_0959 1_0968 1_0654 1_0400 1_0953 1_0444 1_1027 1_0139 1_0207 1_1369 1_0938 1_0604 1_0831 1_1075 1_1109 1_1085 1_1087 1_0352 1_0265 1_0984 1_0380 1_1162 1_0594 1_0388 1_1134 1_0345 1_0718 1_1452 1_0964 1_0331 1_1015 1_1513 1_0404 1_0900 1_0209 1_0769 1_1522 1_0812 Biomass1_0491 1_0820 1_0772 1_1079 1_0893 1_0381 1_0194 1_1058 1_1106 1_0619 1_1292 1_1121 1_0707 Heat1_0201 1_0618 1_0464 1_1500 1_0197 1_1231 1_0121 1_0136 1_0093 1_0776 1_1241 1_0990 1_0373 1_1028 1_0569 1_0921 1_0681 1_0601 1_1412 1_1287 1_0951 1_0102 1_0882 1_0236 1_0878 1_0593 1_1116 1_0105 1_1047 1_0303 1_0301 1_0656 1_1375 1_0626 1_0989 1_0234 Mac1_1251 1_0199 1_0946 1_0180 1_1073 1_1299 1_1065 1_1144 1_0143 1_0436 1_0175 1_0655 1_0539 LG3 1_0364 1_0052 Yield1_0054 1_0854 1_0188 1_0342 1_0456 1_0803 1_0973 1_1032 1_1147 1_0504 1_0382 1_1148 1_0397 1_0969 1_0314 1_0321 1_0976 1_0673 1_0672 1_0890 1_0190 1_0572 1_0502 1_1360 1_1499 1_0580 1_1138 1_1034 1_0155 1_0082 1_0756 1_1445 1_0847 1_0774 1_1221 1_1242 1_0027 1_0153 1_1261 1_0535 1_1092 1_0646 1_0874 1_0826 1_0692 1_0403 1_0106 1_0678 1_1209 1_0117 1_0128 1_1316 1_0157 1_0038 1_0910 1_1013 1_0992 1_0083 1_0417 1_0349 1_0398 1_0856 1_0543 1_0699 1_0804 1_0275 1_0304 1_0200 1_0746 1_0122 1_0267 1_0407 1_0508 1_0875 1_1146 1_1319 1_1191 LG4 1_1003 1_0045 1_0684 Yield1_0309 1_1132 1_0442 1_1366 1_1232 1_0605 1_0095 1_0335 1_0806 1_0292 1_0789 1_0271 1_0507 1_0979 1_1001 1_0478 1_0624 1_0173 1_0819 1_0452 1_0557 1_1492 1_0191 1_0273 1_0510 1_0662 1_0986 1_0030 1_0872 1_0800 1_0040 1_0362 1_0877 1_0419 1_0578 1_1359 1_0926 1_0242 1_0839 1_1419 1_0119 1_1253 1_1243 1_1095 1_0251 1_0346 1_0677 1_1533 1_0205 1_0081 1_0225 1_0399 1_0127 1_1322 1_0032 1_0193 1_0287 1_1128 1_0120 1_0945 1_0661 1_0866 1_0226 1_0037 1_0879 1_0924 1_0548 1_0495 1_0998 1_0588 1_0379 1_0099 1_0889 1_0935 1_0579 1_0231 1_0387 1_0974 1_1401 1_0165 1_0004 1_0923 1_1172 1_0078 1_1165 1_1507 1_0374 1_1130 1_0733 LG5 1_0962 1_0323 1_0691 1_0307 1_0172 1_0174 1_1333 1_1368 1_0300 1_0635 1_0690 1_0751 1_0908 1_0927 1_1331 1_1530 1_0024 1_0823 1_1403 1_0066 1_1515 1_1226 1_1097 1_0432 1_0074 1_0732 1_0332 1_0485 1_0084 1_0825 1_1082 1_0454 1_0216 1_0369 1_0919 1_1496 1_0186 1_0688 1_0675 1_0939 1_0224 1_0871 1_1343 1_0911 1_0830 1_0660 1_1381 1_0895 1_1077 1_1363 1_0897 1_0860 1_1484 1_1107 1_0704 1_0544 1_1443 1_0148 1_0290 1_1020 1_0701 1_0026 1_1090 1_0538 1_0794 1_0124 1_1244 1_1080 1_0760 1_1194 Heat1_1367 1_0437 1_1298 1_0015 1_0664 1_0943 1_0018 1_1012 1_0706 1_0639 1_0975 1_1042 1_0522 1_0880 1_0123 1_0541 1_1043 1_0010 1_0347 1_0765 1_0014 1_0736 1_1271 1_0542 1_0326 1_0514 1_0933 1_0426 1_0367 1_0171 1_1486 1_1508 1_0650 1_1273 1_0947 1_1007 LG6 Heat 1_0881 1_1521 1_0261 1_0763 1_1418 1_1014 1_0006 1_1266 1_1446 1_0719 1_0198 1_1141 1_1302 1_0711 1_1536 1_0529 1_0439 1_0278 1_0723 1_0126 1_0047 Yield1_0631 1_1215 1_1026 1_0385 1_0659 1_1510 1_1414 Drought1_0561 1_0564 1_0644 Staygreen1_1482 1_0168 1_0023 1_0384 1_0906 1_0912 1_1472 1_0755 1_0196 Aphid1_0708 1_0663 1_1057 1_0477 1_1035 1_0648 1_0696 1_0917 1_0228 1_0641 1_0270 1_0884 1_1186 1_0621 1_0392 1_1060 1_0019 1_0469 1_0632 1_0883 1_1315 1_0864 1_1113 1_0294 1_0576 1_0559 1_0824 1_0056 1_0305 1_0944 1_1249 1_1465 1_0039 1_0248 1_0016 1_1135 LG7 1_0519 1_1341 1_0842 1_0858 1_0298 1_0022 1_1370 1_0302 1_0558 1_1362 1_0394 1_0813 1_1008 1_0451 1_0771 1_0567 1_0141 1_0410 1_0762 1_0131 1_0351 1_0918 1_1185 1_1361 1_0807 1_1168 1_1123 1_0665 1_1284 1_0044 1_0524 1_0649 1_0797 1_0255 1_1260 1_1099 1_0076 1_0643 1_1101 1_0801 1_0892 1_0530 1_0438 1_0616 1_1218 1_0353 1_0838 1_0306 1_1374 1_0957 1_0586 1_0566 1_0832 1_1199 1_0187 1_0250 1_1252 1_0375 1_1246 1_0750 1_0241 1_0967 1_0058 1_1529 1_1198 1_0402 1_1393 1_1169 1_0167 1_0233 1_0324 LG8 1_0213 1_1202 1_1016 1_1167 1_0088 1_0668 1_0720 1_0712 1_1347 Nematode1_0487 1_0949 1_0965 1_1208 1_0246 1_0867 1_0795 1_0857 1_0377 1_0389 1_0999 1_1236 1_0728 1_0097 1_0651 1_0987 1_0448 1_0221 1_1159 1_0634 1_1038 1_0051 1_0101 1_0112 1_0090 1_0338 1_0001 1_1491 1_0035 1_0500 1_1192 1_1291 1_0048 1_0371 1_0266 1_0025 1_0480 1_0565 1_1217 1_0179 1_0259 1_1408 1_0421 1_0008 1_0473 1_0235 1_1382 1_1460 1_0158 1_0137 1_1188 1_0431 1_0752 1_0358 1_0214 1_0254 1_1467 1_0425 1_0257 1_1255 1_0474 1_1337 1_0276 1_0958 1_0703 1_0948 1_1069 1_1045 LG9 1_0356 1_1089 1_1409 1_1407 1_0977 1_1120 1_1118 1_1189 1_0288 1_0493 1_0036 1_0401 1_1081 1_1254 1_0330 1_1509 1_1478 1_1225 1_0111 1_1126 1_0109 1_0002 1_0329 1_1017 1_1402 1_0077 1_0780 1_1098 1_0341 1_0416 1_1049 1_1520 1_0981 1_0865 1_1076 1_1444 1_1025 1_0587 1_0628 Yield1_0050 1_0598 Drought1_0501 1_1018 1_0833 1_0739 Staygreen1_0065 1_0754 1_0537 1_0930 1_0281 1_0554 1_1356 1_1453 1_0354 1_0457 1_0053 1_0249 1_0730 1_0952 1_1062 1_0161 1_1041 1_0003 1_0406 1_0583 1_1430 1_0960 1_0007 1_1281 1_0060 1_1263 1_0420 1_0851 1_0368 1_0446 1_0230 1_0282 1_0682 1_0142 1_0861 1_1094 1_1434 1_0107 1_0617 1_0862 1_0239 LG10 1_0940 1_0886 1_0702 1_1052 1_0603 1_0905 1_0134 1_0531 1_0805 1_0894 1_1164 1_0125 Nematode1_0414 1_1390 1_0970 1_0961 1_0028 1_0802 1_1124 1_0033 1_1223 1_0722 1_0339 1_0563 1_1237 1_1388 1_0818 1_0996 1_0043 1_0096 1_0110 1_0550 1_1214 1_1398 1_0600 1_0574 1_0212 1_0859 1_0954 1_1345 1_1327 1_0486 1_0966 1_0311 1_1103 1_0932 1_0494 1_0274 1_0637 1_0955 1_1004 1_0013 1_0608 1_1440 1_1137 1_0562 1_0666 1_0506 1_1197 1_0322 1_0547 1_0629 1_0606 1_0069 1_1377 1_0422 1_0816 1_1180 1_0553 1_0787 1_1417 LG11 0 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
- 18. CB27 (tolerant) x IT82E-18 (sensitive) Tolerant RIL Sensitive RIL 3d. Heat tolerance QTL identified in elite RILs
- 19. CB27 (sensitive) x IT97K-556-6 (resistant) SR 3d. Aphid resistance QTL identified in elite RILs S
- 20. Activity 4 Products. Capacity Building Two PhD students • Senegal (Penda Sarr – enrolled 2011 at Anta Diop Chiekh University, Dakar, Senegal) • Mozambique (Arsenio Ndeve – enrolled Winter 2012 at UCR) • Jointly supported by GCP and USAID CRSP • MABC and MARS breeding PhD students at WACCI • Burkina Faso (Joseph Batieno) – MABC project; supported by GCP Capacity Building funds • Ken Fafa – using KBio SNPs for cowpea seed size MSc students at E. Mondlane U, Mozambique • Mentoring in plant breeding with Rogerio Chiulele
- 21. Activity 5 Products: Data Curation & Storage • TL-1 datasets – Provided genotype datasets to GCP curators (Trushar) • 1536-SNP Illumina platform • ~650 germplasm accessions • Includes almost all MARS and MABC parents – Organized phenotype datasets: UCR in collaboration with Sam Ofodile at IITA • uniform naming conventions, file structure, error detection • 34 cowpea phenotyping datasets standardized at UCR (I Flores) and sent to IITA (S Ofodile) – Added historical pedigrees of IITA lines & pedigrees of TL-1 materials to IITA/GCP database