Table 2 Consistent SNPs across all locations identified for the flowering trait by three or more multi-locus GWAS models
Location | SNP id | LOD/P-value | R2 (%) | Contigid | Alleles | Position | Models* |
|---|---|---|---|---|---|---|---|
Bikaner2021 | SNP4779 | 5.54 to 9.80 | 5.65 to 11.74 | 65,980 | T/A | 8 | 1,2,3,4,5,6,7 |
SNP2396 | 3.08 to 3.45 | 4.12 to 6.67 | 34,123 | G/T | 179 | 3,4,5,6,7 | |
SNP2234 | 5.74 to 6.90 | 10.08 to 10.61 | 31,981 | A/C | 8 | ||
SNP3620 | 4.45 to 6.20 | 12.10 to 13.83 | 51,790 | A/G | 122 | 2,3,4,7 | |
SNP5026 | 0.000331 to 0.000646 | - | 69,414 | C/A | 24 | 4,6,7 | |
SNP6240 | 0.000471 to 0.000542 | - | 90,821 | T/C | 40 | 5,6,7 | |
Bikaner2022 | SNP858 | 4.90 to 13.72 | 7.70 to 16.83 | 9445 | C/T | 194 | 1,2,4,5,7 |
SNP6703 | 5.0 to 13.50 | 8.24 to 13.31 | 99,723 | C/T | 60 | 1,2,3,4,5,7 | |
SNP6919 | 3.32 to 4.17 | 5.84 to 10.63 | 104,203 | A/G | 15 | 2,3,4,5,6,7 | |
SNP4472 | 1.41E-05 to 0.000525 | - | 62,079 | C/T | 10 | 5,6,7 | |
SNP4735 | 2.48E-05 to 0.000524 | - | 65,331 | G/A | 198 | ||
SNP9065 | 4.82E-06 to 0.000951 | - | 1,416,336 | C/T | 124 | ||
Jodhpur2019 | SNP268 | 3.90 to 5.93 | 2.51 to 2.97 | 1890 | A/G | 102 | 1,3,4,5,6,7 |
SNP3620 | 3.26 to 4.51 | 6.92 to 12.84 | 51,790 | A/G | 122 | 2,3,4,6 | |
SNP4779 | 5.56 to 7.96 | 7.774 to 10.59 | 65,980 | T/A | 8 | 1,2,3,4,5,6,7 | |
SNP6919 | 3.43 to 4.32 | 6.78 to 11.40 | 104,203 | A/G | 15 | 2,3,4,5,6,7 | |
SNP9076 | 4.19 to 4.93 | 7.57 to 9.49 | 1,436,316 | C/T | 155 | ||
SNP4701 | 4.55 to 5.83 | 3.00 to 3.74 | 64,944 | GA | 98 | 2,3,4 | |
SNP5572 | 6.29E-05 to 0.000578 | - | 80,466 | G/A | 48 | 3,6,7 | |
SNP1503 | 7.36E-06 to 9.01E-05 | - | 19,323 | C/A | 17 | 5,6,7 | |
SNP279 | 5.00E-05 to 0.000372 | - | 2196 | G/A | 277 | ||
Jodhpur2021 | SNP4963 | 3.62 to 5.20 | 1.96 to 4.02 | 68,557 | A/G | 178 | 1,2,3,4,5,6,7 |
SNP3448 | 3.72 to 5.32 | 4.19 to 4.95 | 49,714 | C/T | 131 | 2,3,4 | |
SNP6972 | 3.10 to 3.52 | 3.51E-10 to 3.41 | 105,244 | C/A | 298 | 1,3,6 | |
SNP6349 | 3.58 to 5.10 | 4.96 to 8.19 | 92,715 | T/C | 197 | 1,2,4 | |
SNP3112 | 3.06 to 3.32 | 2.06 to 4.52 | 43,947 | G/A | 171 | 2,4,5 | |
SNP5059 | 3.07 to 4.16 | 2.85 to 2.86 | 70,169 | G/A | 4 | 2,3,7 | |
Jodhpur2022 | SNP4779 | 11.21–17.04 | 10.16 to 18.83 | 65,980 | T/A | 8 | 1,2,3,4,5,6,7 |
SNP8592 | 3.74 to 5.37 | 1.80 to 6.25 | 469,510 | G/A | 80 | 1,2,3,4,5,7 | |
SNP4936 | 3.71 to 3.97 | 1.84 to 5.64 | 67,953 | C/T | 114 | 1,3,4,5,6,7 | |
SNP6721 | 3.05 to 6.53 | 5.41 to 7.46 | 100,323 | A/T | 34 | 2,4,5,6 | |
SNP6793 | 0.000178 to 0.000831 | - | 102,366 | T/A | 110 | 4,5,7 | |
SNP6919 | 3.41E-06 to 0.000431 | - | 104,203 | A/G | 15 | 2,5,6 | |
SNP1371 | 8.37E-06 to 0.000631 | - | 17,452 | A/G | 155 | 5,6,7 |