Table 3.
List of significant markers associated with agronomic traits from genome-wide association analysis of 309 sorghum accessions using 3143 SNPs with MAF greater than 0.05.
| Trait | SNP | Alleles | Chr | Position | MAF | P.value | FDR | PVE (%) | Model |
|---|---|---|---|---|---|---|---|---|---|
| DTF | sbi318688 | G/A | 1 | 8066218 | 0.26 | 4.14E-06 | 0.002842 | 2.26 | farmCPU |
| 5.89E-09 | 9.26E-06 | 1.45 | BLINK | ||||||
| sbi982537 | G/T | 1 | 22275540 | 0.12 | 1.03E-05 | 0.004032 | 2.38 | farmCPU | |
| sbi4023260 | G/C | 2 | 13293723 | 0.43 | 2.07E-07 | 0.000217 | 2.09 | BLINK | |
| sbi10226120 | A/G | 3 | 56322246 | 0.29 | 9.58E-06 | 0.004032 | 3.58 | farmCPU | |
| sbi10372954 | T/C | 3 | 59472033 | 0.13 | 2.24E-06 | 0.002345 | 0.91 | farmCPU | |
| sbi10438246 | C/A | 3 | 60811994 | 0.06 | 7.88E-11 | 2.48E-07 | 23.95 | farmCPU | |
| 9.32E-10 | 2.93E-06 | 35.23 | BLINK | ||||||
| sbi17364528 | T/G | 5 | 61608548 | 0.07 | 3.24E-07 | 0.000255 | 9.89 | BLINK | |
| sbi17966906 | C/A | 6 | 1001235 | 0.29 | 5.84E-06 | 0.003064 | 1.83 | BLINK | |
| snp_sb001000704585 | A/T | 6 | 48682625 | 0.32 | 9.37E-06 | 0.004032 | 1.00 | farmCPU | |
| snp_sb042060813825 | A/G | 7 | 39653062 | 0.07 | 2.05E-06 | 0.002345 | 2.59 | farmCPU | |
| sbi24678469 b | C/G | 8 | 5242533 | 0.09 | 1.51E-06 | 0.00095 | 3.97 | BLINK | |
| sbi30754782 | G/T | 10 | 9494280 | 0.26 | 4.52E-06 | 0.002842 | 1.96 | farmCPU | |
| PH | sbi62970 | C/T | 1 | 1495213 | 0.11 | 1.45E-05 | 0.0046 | 4.35 | farmCPU |
| sbi194467 | G/A | 1 | 4778713 | 0.40 | 8.41E-06 | 0.0033 | 0.71 | BLINK | |
| sbi7769289 | C/T | 3 | 10836535 | 0.08 | 1.20E-05 | 0.004207 | 3.11 | farmCPU | |
| 2.70E-10 | 4.25E-07 | 6.32 | BLINK | ||||||
| sbi7901589 | A/G | 3 | 13494213 | 0.38 | 1.85E-06 | 0.0012 | 6.32 | farmCPU | |
| sbi13732034 a | C/T | 4 | 54108806 | 0.19 | 1.91E-07 | 0.000201 | 2.21 | farmCPU | |
| 1.47E-06 | 0.000923 | 3.21 | BLINK | ||||||
| sbi17260778 | G/A | 5 | 59844243 | 0.42 | 1.89E-06 | 0.0010 | 2.46 | BLINK | |
| sbi20359577 | C/T | 6 | 48007508 | 0.13 | 3.56E-06 | 0.0016 | 1.75 | farmCPU | |
| sbi20792384 | G/T | 6 | 57704110 | 0.31 | 1.29E-12 | 4.05E-09 | 1.62 | farmCPU | |
| 1.77E-10 | 4.25E-07 | 1.43 | BLINK | ||||||
| sbi24138103 | G/T | 7 | 59997937 | 0.12 | 1.15E-06 | 0.0009 | 1.59 | BLINK | |
| sbi24291993 | T/C | 7 | 63300346 | 0.13 | 2.46E-06 | 0.0011 | 4.58 | BLINK | |
| sbi24668980 | G/A | 8 | 5053406 | 0.09 | 2.56E-06 | 0.001343 | 3.77 | farmCPU | |
| 5.97E-07 | 0.000627 | 1.28 | BLINK | ||||||
| sbi30188088 | C/G | 9 | 56601353 | 0.19 | 2.76E-07 | 0.0002 | 0.79 | farmCPU | |
| sbi30546176 | C/T | 10 | 5270775 | 0.11 | 7.45E-06 | 0.0029 | 1.55 | farmCPU | |
| sbi30645260 | A/G | 10 | 7303004 | 0.06 | 4.02E-08 | 0.0001 | 6.75 | farmCPU | |
| PALH | sbi3208134 | C/T | 1 | 78277352 | 0.09 | 2.26E-09 | 7.10E-06 | 5.44 | farmCPU |
| 1.30E-10 | 4.01E-07 | 9.62 | BLINK | ||||||
| sbi7353016 | G/A | 3 | 1905405 | 0.10 | 1.54E-05 | 0.006929 | 4.03 | BLINK | |
| sbi7686697 | A/G | 3 | 9057564 | 0.42 | 2.69E-06 | 0.00141 | 2.47 | BLINK | |
| sbi21359653 | A/G | 7 | 8646573 | 0.36 | 2.55E-10 | 4.01E-07 | 11.25 | BLINK | |
| sbi24678469 b | C/G | 8 | 5242533 | 0.09 | 2.67E-07 | 0.000228 | 3.24 | BLINK | |
| sbi30118348 | T/A | 9 | 54963433 | 0.34 | 5.18E-07 | 0.000326 | 1.74 | BLINK | |
| sbi30169733 | A/T | 9 | 56240567 | 0.26 | 1.41E-06 | 0.002214 | 2.87 | farmCPU | |
| 2.89E-07 | 0.000228 | 18.91 | BLINK | ||||||
| PAWD | sbi2029574 | G/T | 1 | 52905292 | 0.20 | 6.67E-06 | 0.005249 | 4.80 | farmCPU |
| 2.43E-08 | 2.55E-05 | 0.44 | BLINK | ||||||
| sbi2393610 | A/T | 1 | 59685990 | 0.07 | 9.96E-08 | 0.000313 | 10.42 | farmCPU | |
| 2.01E-13 | 6.33E-10 | 23.31 | BLINK | ||||||
| sbi3026667 | T/C | 1 | 73774042 | 0.21 | 2.59E-11 | 0.005249 | 4.51 | BLINK | |
| sbi3655489 | A/T | 2 | 6615133 | 0.30 | 6.97E-07 | 0.002386 | 1.45 | BLINK | |
| sbi6496334 | G/T | 2 | 59698705 | 0.22 | 1.90E-06 | 0.002902 | 1.34 | BLINK | |
| sbi8085609 | C/G | 3 | 16868775 | 0.07 | 5.49E-06 | 0.005249 | 2.19 | farmCPU | |
| 6.07E-06 | 0.002386 | 10.93 | BLINK | ||||||
| sbi10162413 | T/C | 3 | 55078201 | 0.25 | 1.35E-05 | 0.000438 | 0.94 | BLINK | |
| sbi10836055 | T/C | 3 | 70604368 | 0.19 | 4.19E-06 | 2.55E-05 | 6.37 | farmCPU | |
| sbi17331791 | G/C | 5 | 61061450 | 0.21 | 5.14E-07 | 0.004239 | 1.57 | BLINK | |
| sbi20777395 | A/G | 6 | 57341190 | 0.18 | 2.29E-06 | 6.33E-10 | 2.05 | BLINK | |
| sbi24445033 | G/T | 8 | 1016470 | 0.27 | 8.30E-06 | 4.08E-08 | 2.23 | BLINK | |
| PAWT | sbi13732034a | C/T | 4 | 54108806 | 0.19 | 1.46E-06 | 0.002048 | 5.91 | BLINK |
| sbi17687423 | T/C | 5 | 67739573 | 0.08 | 3.04E-07 | 0.000956 | 7.01 | BLINK | |
| sbi21079990 | A/G | 7 | 2945057 | 0.36 | 1.95E-06 | 0.002048 | 1.65 | BLINK | |
| sbi21265823 | T/C | 7 | 6671420 | 0.30 | 1.50E-05 | 0.026887 | 8.03 | farmCPU | |
| sbi30583046c | C/G | 10 | 6047480 | 0.50 | 1.01E-05 | 0.00798 | 2.69 | BLINK | |
| GY | sbi3833 | T/C | 1 | 80269 | 0.2 | 5.43E-06 | 0.005837 | 3.10 | BLINK |
| sbi17653919 | G/C | 5 | 67092426 | 0.1 | 1.59E-05 | 0.012496 | 3.12 | BLINK | |
| sbi17789352 | G/A | 5 | 69674648 | 0.2 | 3.13E-06 | 0.009845 | 11.49 | farmCPU | |
| snp_sb001001045636 | A/G | 10 | 5151950 | 0.1 | 5.57E-06 | 0.005837 | 6.69 | BLINK | |
| sbi30583046c | C/G | 10 | 6047480 | 0.5 | 1.00E-06 | 0.003155 | 7.23 | BLINK |
MAF, Minor allele frequency; Chr, chromosome; PVE, Phenotypic variance explained; FDR, False discovery rate; PH, Plant height; DTF, Days to flowering; PALH, Panicle length; PAWD, Panicle width; PAWT, Panicle weight; GY, Grain yield. Favorable alleles are given in bold. SNP associated with more than one trait are shown in bold, and those sharing a superscript are the same.