Table 3.
Frequencies and marker prediction effects of various haplotypes associated with tuber yield (kg plant-1) and reaction to yam mosaic virus infection (AUDPC value)
| Traits | Markers | Hap | Seq | Freq | Adjusted probability | Prob. Adj. significance |
|---|---|---|---|---|---|---|
| Yield | chr04_6236404 | Hap1 | CCCT | 0.475 | 3.74 e-05 | **** |
| Hap2 | CCTT | 0.296 | 7.11 e-07 | **** | ||
| Hap3 | CTTT | 0.228 | 0.001 | *** | ||
| chr04_8196378 | Hap1 | CCCT | 0.481 | 0.218 | ns | |
| Hap2 | CCTT | 0.364 | 0.041 | * | ||
| Hap3 | CTTT | 0.154 | 0.218 | ns | ||
| chr04_18269860 | Hap1 | AAAC | 0.328 | 0.399 | ns | |
| Hap2 | AACC | 0.359 | 0.814 | ns | ||
| Hap3 | ACCC | 0.312 | 0.814 | ns | ||
| chr04_23401186 | Hap1 | AAAG | 0.274 | 0.029 | * | |
| Hap2 | AAGG | 0.396 | 0.001 | *** | ||
| Hap3 | AGGG | 0.330 | 0.619 | ns | ||
| chr05_24237388 | Hap1 | CCCT | 0.367 | 0.020 | * | |
| Hap2 | CCTT | 0.316 | 3.57 e-11 | **** | ||
| Hap3 | CTTT | 0.317 | 1.02 e-05 | **** | ||
| chr05_24682916 | Hap1 | AAAC | 0.295 | 0.921 | ns | |
| Hap2 | AACC | 0.305 | 0.044 | * | ||
| Hap3 | ACCC | 0.400 | 0.043 | * | ||
| chr08_7046574 | Hap1 | AAAC | 0.142 | 0.294 | ns | |
| Hap2 | AACC | 0.423 | 1.25 e-11 | **** | ||
| Hap3 | ACCC | 0.435 | 2.16 e-08 | **** | ||
| chr08_10135940 | Hap1 | CCCG | 0.217 | 0.363 | ns | |
| Hap2 | CCGG | 0.326 | 0.522 | ns | ||
| Hap3 | CGGG | 0.457 | 0.522 | ns | ||
| chr10_1317508 | Hap1 | CCCT | 0.363 | 0.079 | ns | |
| Hap2 | CCTT | 0.359 | 0.713 | ns | ||
| Hap3 | CTTT | 0.278 | 0.246 | ns | ||
| chr10_1571815 | Hap1 | CCCT | 0.144 | 0.873 | ns | |
| Hap2 | CCTT | 0.362 | 0.873 | ns | ||
| Hap3 | CTTT | 0.494 | 0.978 | ns | ||
| chr13_13467988 | Hap1 | CCCT | 0.364 | 0.912 | ns | |
| Hap2 | CCTT | 0.365 | 6.12 e-04 | *** | ||
| Hap3 | CTTT | 0.270 | 0.001 | *** | ||
| chr14_11301309 | Hap1 | AAAG | 0.110 | 0.705 | ns | |
| Hap2 | AAGG | 0.393 | 0.386 | ns | ||
| Hap3 | AGGG | 0.498 | 1.01 e-20 | **** | ||
| chr14_11128124 | Hap1 | CCGG | 0.414 | 6.59 e-18 | **** | |
| chr15_5858214 | Hap1 | CCCT | 0.394 | 0.003 | ** | |
| Hap2 | CCTT | 0.192 | 0.242 | ns | ||
| Hap3 | CTTT | 0.315 | 0.057 | ns | ||
| chr17_15363223 | Hap1 | AAAT | 0.539 | 1.20 e-13 | **** | |
| Yield | chr17_19041958 | Hap1 | CCCT | 0.146 | 0.516 | ns |
| Hap2 | CCTT | 0.281 | 0.516 | ns | ||
| Hap3 | CTTT | 0.370 | 0.799 | ns | ||
| chr19_9446619 | Hap1 | AAAG | 0.349 | 0.002 | ** | |
| Hap2 | AAGG | 0.513 | 2.94 e-06 | **** | ||
| Hap3 | AGGG | 0.059 | 0.872 | ns | ||
| YMV | chr03_6338751 | Hap1 | GGGT | 0.427 | 1.000 | ns |
| Hap2 | GGTT | 0.320 | 1.000 | ns | ||
| Hap3 | GTTT | 0.466 | 1.000 | ns | ||
| chr10_1116193 | Hap1 | AAAG | 0.226 | 0.254 | ns | |
| Hap2 | AAGG | 0.309 | 0.003 | ** | ||
| Hap3 | AGGG | 0.465 | 6.75 e-07 | **** | ||
| chr15_3906069 | Hap1 | AAAC | 0.214 | 0.882 | ns | |
| Hap2 | AACC | 0.281 | 0.882 | ns | ||
| Hap3 | ACCC | 0.412 | 0.882 | ns | ||
| chr16_1482029 | Hap1 | AAAT | 0.307 | 0.096 | ns | |
| Hap2 | AATT | 0.424 | 2.01 e-04 | *** | ||
| Hap3 | ATTT | 0.576 | 0.006 | ** | ||
| chr05_30671001 | Hap1 | AAAG | 0.365 | 1.000 | ns | |
| Hap2 | AAGG | 0.265 | 1.000 | ns | ||
| Hap3 | AGGG | 0.369 | 1.000 | ns |
ns=non-significant, *, **, ***, and **** indicate significant association between haplotypes and markers