Table 1.
Associated markers for flowering, maturity and seed weight predicted using phenotypic data of Almora location in the year 2020
| Marker IDa | SNPc | Transcript ID | Position (in bp) | Modelsb | Trait(s) | -log10 (P)/ LODc | MAFc | R2 |
|---|---|---|---|---|---|---|---|---|
| SVUTC32100_1612 | C/T | VUTC32100 | 1612 | 6,8,5 | Flowering | LOD: 4.52 to 7.07 | 0.260 | 5.63 to 11.99 |
| SVUTC02300_1585 | C/A | VUTC02300 | 1585 | 6,7 | Flowering | LOD: 6.15 to 11.00 | 0.464 | 7.10 to 5.38 |
| SVUTC22319_438 | C/T | VUTC22319 | 438 | 6,7 | Flowering | LOD: 3.84 to 7.72 | 0.355 | 4.72 to 9.66 |
| SVUTC06910_1648 | C/T | VUTC06910 | 1648 | 4,3,2,1,9,10 | Maturity | -log10(P): 6.31 to 13.33 | 0.055 | 38 to 47 |
| SVUTC06910_1702 | G/T | VUTC06910 | 1702 | 4, 3,2,1,10 | Maturity | -log10(P): 6.31 to 13.33 | 0.055 | 38 to 47 |
| SVUTC06910_1746 | C/G | VUTC06910 | 1746 | 4,3,2,1,10 | Maturity | -log10(P): 6.31 to 13.33 | 0.055 | 38 to 47 |
| SVUTC06910_177 | C/G | VUTC06910 | 177 | 4,3,2,1 | Maturity | -log10(P): 6.79 to 13.51 | 0.063 | 37 to 49 |
| SVUTC02283_1297 | G/T | VUTC02283 | 1297 | 4,2,1 | Maturity | -log10(P): 6.07 to 10.96 | 0.092 | 28 to 41 |
| SVUTC07229_692 | T/C | VUTC07229 | 692 | 6,5,8 | Maturity | LOD: 5.68 to 7.24 | 0.220 | 23 to 24 |
| SVUTC08788_874 | A/G | VUTC08788 | 874 | 3,2,1 | Maturity | -log10(P): 6.20 to 11.35 | 0.057 | 29 to 43 |
| SVUTC21395_469 | A/G | VUTC21395 | 469 | 5,8,6 | Maturity | LOD: 3.56 to 6.03 | 0.200 | 8.33 to 18.24 |
| SVUTC27187_1237 | C/T | VUTC27187 | 1237 | 3,2,1 | Maturity | LOD: 6.15 to 11.00 | 0.060 | 30 to 43 |
| SVUTC27441_1674 | A/C | VUTC27441 | 1674 | 3,2,1 | Maturity | -log10(P): 5.99 to 10.97 | 0.060 | 28 to 41 |
| SVUTC06910_1616 | C/G | VUTC06910 | 1616 | 7,1 | Maturity |
-log10(P): 6.61 LOD: 4.07 |
0.056 | 10 to 27 |
| SVUTC16925_1108 | T/C | VUTC16925 | 1108 | 8,6 | Maturity | LOD: 6.02 to 7.39 | 0.262 | 13.33 to 14.64 |
| SVUTC31321_227 | A/C | VUTC31321 | 227 | 8,10 | Maturity |
log10(P): 6.30 LOD: 5.43 |
0.100 | 16.84 |
| SVUTC34182_2284 | C/T | VUTC34182 | 2284 | 6,10 | Maturity |
log10(P): 6.31 LOD: 3.01 |
0.306 | 4.60 |
| SVUTC25856_1400 | T/G | VUTC25856 | 1400 | 5,8,6 | Maturity, Seed weight | LOD: 3.99 to 5.88 | 0.214 | 7.06 to 13.22 |
| SVUTC06074_3949 | G/A | VUTC06074 | 3949 | 8,6 | Seed weight | LOD: 3.85 to 6.63 | 0.146 | 9.59 to 11.35 |
| SVUTC12822_2877 | A/G | VUTC12822 | 2877 | 8,6 | Seed weight | LOD: 4.36 to 5.59 | 0.191 | 6.99 to 7.43 |
| SVUTC21543_375 | C/T | VUTC21543 | 375 | 8,6 | Seed weight | LOD: 3.5 to 5.46 | 0.247 | 8.00 to 11.45 |
| SVUTC25312_5309 | G/A | VUTC25312 | 5309 | 8,6 | Seed weight | LOD: 9.18 to 9.86 | 0.468 | 6.90 to 12.33 |
| SVUTC25491_6046 | T/C | VUTC25491 | 6046 | 8,6 | Seed weight | LOD: 7.91 to 8.72 | 0.261 | 3.15 to 4.06 |
| SVUTC30884_3008 | T/G | VUTC30884 | 3008 | 8,6 | Seed weight | LOD: 6.03 to 11.58 | 0.205 | 10.51 to 26.26 |
aThe markers highlighted in yellow are associated with more than one trait
b1. GLM (Q), 2. GLM (PCA)], 3. MLM (Q + K), 4. MLM (PCA + K), 5. mrMLM, 6. FASTmrMLM, 7. FASTmrEMMA, 8. ISIS EMBLASSO, 9. FarmCPU, 10. BLINK
cSNP single nucleotide polymorphism, LOD logarithm of the odds, MAF minor allele frequency