Table 3.
Significant SNPs identified under Striga infested condition.
| Trait name | SNP | Chr | Position (bp) | LOD | PVE (%) | Favorable allele | Methods |
|---|---|---|---|---|---|---|---|
| YLDIN_G | S4_164335765 | 4 | 164335765 | 7.18 | 13.36 | A | 1, 2 |
| S9_1994432 | 9 | 1994432 | 7.21 | 3.21 | G | 4 | |
| S10_1784894 | 10 | 1784894 | 7.39 | 3.58 | C | 4 | |
| Striga damage rating at 8 WAP | S1_18512344 | 1 | 18512344 | 10.76 | 14.19 | T | 1 |
| S2_14081759 | 2 | 14081759 | 8.26 | 7.89 | A | 1 | |
| S2_160791711 | 2 | 160791711 | 7.28 | 3.35 | A | 1 | |
| S2_219240910 | 2 | 219240910 | 11.31 | 8.05 | G | 3 | |
| S4_160459526 | 4 | 160459526 | 6.07 | 3.83 | C | 1 | |
| S5_70442824 | 5 | 70442824 | 6.76 | 3.22 | C | 2 | |
| S5_216138908 | 5 | 216138908 | 6.81 | 6.67 | C | 4 | |
| S6_25428338 | 6 | 25428338 | 6.58 | 0.142 | A | 4 | |
| S10_25285761 | 10 | 25285761 | 11.87 | 6.57 | G | 2 | |
| S10_2743583 | 10 | 2743583 | 9.86 | 0.24 | C | 4 | |
| S10_68324912 | 10 | 68324912 | 11.79 | 1.32 | C | 4 | |
| Striga damage rating at 10 WAP | S1_284192573 | 1 | 284192573 | 8.54 | 10.40 | G | 1, 2, 3 |
| S1_10576247 | 1 | 10576247 | 6.45 | 10.00 | A | 1, 2 | |
| S2_190557148 | 2 | 190557148 | 6.02 | 4.13 | T | 1 | |
| S2_99667127 | 2 | 99667127 | 7.82 | 4.82 | A | 1, 2 | |
| S2_160791711 | 2 | 160791711 | 6.18 | 4.37 | A | 3 | |
| S2_188120710 | 2 | 188120710 | 13.76 | 6.47 | A | 4 | |
| S5_5623740 | 5 | 5623740 | 6.06 | 13.97 | C | 1 | |
| S7_10795659 | 7 | 10795659 | 6.71 | 7.99 | A | 1, 2 | |
| S10_25285761 | 10 | 25285761 | 6.56 | 5.04 | G | 3 | |
| Emerged Striga plants at 8 WAP | S1_298950342 | 1 | 298950342 | 6.15 | 6.58 | A | 1 |
| S2_135038935 | 2 | 135038935 | 6.67 | 6.66 | G | 3, 4 | |
| S2_208978140 | 2 | 208978140 | 6.82 | 6.97 | C | 3, 4 | |
| S3_74335447 | 3 | 74335447 | 6.21 | 5.54 | A | 1 | |
| S5_148751913 | 5 | 148751913 | 6.41 | 6.21 | A | 3, 4 | |
| S9_7727167 | 9 | 7727167 | 8.32 | 11.51 | G | 1, 2 | |
| S10_125571525 | 10 | 125571525 | 9.28 | 13.08 | G | 1, 2, 4 | |
| S10_90133328 | 10 | 90133328 | 7.75 | 13.58 | T | 1, 2, 4 | |
| Emerged Striga plants at 10 WAP | S2_135038935 | 2 | 135038935 | 6.83 | 12.22 | G | 1, 2 |
| S5_148751913 | 5 | 148751913 | 8.65 | 7.91 | A | 1, 2 | |
| S5_204969099 | 5 | 204969099 | 6.93 | 10.22 | T | 1, 2 | |
| S10_125571525 | 10 | 125571525 | 7.00 | 6.33 | G | 4 |
Methods: Numbers 1 to 4 represents different GWAS methods: 1: mrMLM; 2: FASTmrMLM; 3: FASTmrEMMA; 4 pLARmEB Chr, Chromosome; YLDIN_G, Grain yield; WAP, weeks after planting.