Table 3 Quantitative trait nucleotides (QTNs) associated with germination rate (GR), whole seedling length (WSL) and root length (RL) via mrMLM.
Trait ID | QTN | Env.a | Chr.b | SNP | Position (bp) | QTN effect | LOD score | − log10Pc | R2 (%) | MAF | Genotype |
|---|---|---|---|---|---|---|---|---|---|---|---|
GR | qGR4 | 2018 | 4 | Gm04-8805064 | 8805064 | 0.084 | 6.329 | 7.173 | 7.903 | 0.168 | A |
qGR8-1 | 2018 | 8 | Gm08-12368145 | 12368145 | 0.073 | 7.536 | 8.415 | 9.9567 | 0.383 | A | |
qGR10 | 2018 | 10 | Gm10-2912266 | 2912266 | − 0.052 | 3.314 | 4.029 | 4.3644 | 0.269 | G | |
qGR19-1 | 2018 | 19 | Gm19-45138884 | 45138884 | − 0.055 | 3.096 | 3.797 | 4.2803 | 0.208 | C | |
qGR6 | 2019 | 6 | Gm06-11913935 | 11913935 | − 0.075 | 4.288 | 5.054 | 8.0296 | 0.351 | T | |
qGR8-1 | 2019 | 8 | Gm08-12368145 | 12368145 | 0.071 | 5.418 | 6.230 | 8.4029 | 0.383 | A | |
qGR9 | 2019 | 9 | Gm09-35829245 | 35829245 | − 0.075 | 5.289 | 6.097 | 6.0674 | 0.156 | G | |
qGR16 | 2019 | 16 | Gm16-33529724 | 33529724 | 0.077 | 5.452 | 6.266 | 7.6347 | 0.185 | A | |
qGR2-2 | Combined | 2 | Gm02-2861258 | 2861258 | 0.066 | 3.907 | 4.654 | 7.1115 | 0.311 | T | |
qGR8-1 | Combined | 8 | Gm08-12368145 | 12368145 | 0.062 | 6.741 | 7.597 | 8.9977 | 0.383 | A | |
qGR11 | Combined | 11 | Gm11-9062549 | 9062549 | − 0.059 | 3.532 | 4.259 | 4.0415 | 0.198 | G | |
WSL | qWSL13-1 | 2018 | 13 | Gm13-35394159 | 35394159 | − 0.069 | 4.592 | 5.372 | 8.068 | 0.109 | A |
qWSL14 | 2018 | 14 | Gm14-47884956 | 47884956 | 0.041 | 4.553 | 5.331 | 6.2969 | 0.324 | A | |
qWSL16 | 2018 | 16 | Gm16-18589836 | 18589836 | 0.043 | 5.166 | 5.969 | 4.9986 | 0.191 | G | |
qWSL18-2 | 2018 | 18 | Gm18-51452390 | 51452390 | − 0.025 | 4.073 | 4.828 | 2.6056 | 0.477 | A | |
qWSL20-1 | 2018 | 20 | Gm20-36122830 | 36122830 | − 0.040 | 4.709 | 5.493 | 5.7337 | 0.324 | A | |
qWSL12 | 2019 | 12 | Gm12-2710068 | 2710068 | − 0.063 | 3.655 | 4.388 | 6.4491 | 0.097 | G | |
qWSL13-1 | 2019 | 13 | Gm13-35394159 | 35394159 | − 0.062 | 4.367 | 5.136 | 7.1721 | 0.109 | A | |
qWSL18 | 2019 | 18 | Gm18-224527 | 224527 | 0.050 | 4.625 | 5.405 | 6.0322 | 0.162 | T | |
qWSL13-1 | Combined | 13 | Gm13-35394159 | 35394159 | 0.033 | 4.288 | 5.054 | 8.0296 | 0.351 | A | |
qWSL18-1 | Combined | 18 | Gm18-224527 | 224527 | 0.052 | 6.882 | 7.743 | 6.5292 | 0.162 | T | |
qWSL20-2 | Combined | 20 | Gm20-34381893 | 34381893 | − 0.053 | 5.721 | 6.545 | 8.5594 | 0.214 | A | |
RL | qRL6 | 2018 | 6 | Gm06-12538994 | 12538994 | − 0.072 | 4.716 | 5.500 | 6.0961 | 0.130 | C |
qRL-8 | 2018 | 8 | Gm08-12368145 | 12368145 | 0.061 | 6.624 | 7.477 | 8.4509 | 0.315 | G | |
qRL15-1 | 2018 | 15 | Gm15-14841750 | 14841750 | − 0.089 | 5.418 | 6.230 | 13.4029 | 0.132 | T | |
qRL16-2 | 2018 | 16 | Gm16-17726124 | 17726124 | 0.057 | 4.591 | 5.370 | 5.9049 | 0.223 | C | |
qRL19 | 2018 | 19 | Gm19-31536655 | 31536655 | − 0.062 | 3.246 | 3.956 | 5.0791 | 0.128 | T | |
qRL7-1 | 2019 | 7 | Gm07-6015318 | 6015318 | − 0.102 | 7.625 | 8.508 | 18.6021 | 0.278 | C | |
qRL7-2 | 2019 | 7 | Gm07-6604493 | 6604493 | 0.062 | 6.741 | 7.597 | 7.9977 | 0.383 | A | |
qRL-8 | 2019 | 8 | Gm08-12368145 | 12368145 | 0.055 | 4.033 | 4.786 | 5.6986 | 0.316 | G | |
qRL14 | 2019 | 14 | Gm14-28361034 | 28361034 | 0.058 | 6.385 | 7.230 | 7.451 | 0.483 | G | |
qRL20 | 2019 | 20 | Gm20-40765691 | 40765691 | 0.061 | 5.564 | 6.382 | 6.0109 | 0.237 | G | |
qRL7-1 | Combined | 7 | Gm07-6015318 | 6015318 | − 0.077 | 6.501 | 7.350 | 11.33 | 0.278 | C | |
qRL7-2 | Combined | 7 | Gm07-6604493 | 6604493 | 0.075 | 7.555 | 8.435 | 12.5244 | 0.383 | A | |
qRL-8 | Combined | 8 | Gm08-12368145 | 12368145 | 0.070 | 7.782 | 8.668 | 9.8464 | 0.316 | G | |
qRL13 | Combined | 13 | Gm13-29961821 | 29961821 | − 0.047 | 3.077 | 3.778 | 3.7954 | 0.254 | T | |
qRL16-1 | Combined | 16 | Gm16-5586574 | 5586574 | 0.046 | 3.334 | 4.050 | 4.6205 | 0.376 | G |
