Table 3.
List of significant SNP associations, the genes tagged by significant SNPs and information from the genome wide analysis of sorghum germplasm under cold stress at seedling stage
| Trait | SNP | FDR Adjusted p-Values* | R2 Value ** | Nucleotide Variation | Distance to nearest gene (bp) *** | Nearest Gene ID |
|---|---|---|---|---|---|---|
| CSt_SFW | S6_57170126 | 0.008 | 10.73 | C/G | (−)588 | Sb06g028380 |
| CSt_SFW | S6_57163269 | 0.008 | 10.26 | A/G | 149 | Sb06g028370 |
| CSt _SFW | S6_57302179 | 0.015 | 10.30 | T/C | 0 | Sb06g028540 |
| CSt _SFW | S6_57163127 | 0.015 | 12.62 | A/G | 291 | Sb06g028370 |
| CSt _SFW | S3_47228001 | 0.015 | −17.48 | T/C | 1973 | Sb03g023720 |
| CSt _RFW | S3_59699677 | 0.000 | 0.06 | T/A | 930 | Sb03g031320 |
| CSt _SL | S6_5762763 | 0.171 | 8.75 | T/A | 768 | Sb06g002877 |
| CSt _RL | S2_73739699 | 0.001 | −20.80 | T/A | (−)127 | Sb02g039680 |
| CSt _RL | S9_8614594 | 0.001 | −14.86 | G/A | 2098 | Sb09g006020 |
| CSt _RL | S2_56602226 | 0.001 | −12.79 | G/A | 543 | Sb02g023140 |
| CSt _RL | S2_54575799 | 0.005 | 11.99 | A/G | (+)889 | Sb02g022120 |
| CSt _RL | S4_60946340 | 0.005 | −25.13 | G/C | 569 | Sb04g030940 |
| CSt _RL | S3_16201529 | 0.008 | −16.12 | G/C | 495 | Sb03g013220 |
| CSt _RL | S2_56566217 | 0.010 | 12.65 | C/G | (+)398 | Sb02g023120 |
| CSt_RL | S2_67807062 | 0.015 | −12.04 | C/A | - | - |
| CSt_RL | S2_72583772 | 0.015 | 14.48 | C/T | (+)2810 | Sb02g038300 |
| CSt_RL | S2_72833569 | 0.015 | 12.10 | C/T | (+)2150 | Sb02g038630 |
| CSt_RL | S2_54593968 | 0.019 | 13.13 | A/G | (−)156 | Sb02g022140 |
| CSt_RL | S2_54593969 | 0.019 | 13.13 | A/G | (−)157 | Sb02g022140 |
| CSt_RL | S5_1302419 | 0.019 | 5.84 | C/G | (+)66 | Sb05g001215 |
| CSt_Anth_W−1 | S1_8039999 | 0.022 | −42.27 | G/T | (−)104 | Sb01g009310 |
| CSt_Anth_W−1 | S6_53967668 | 0.001 | −5.71 | T/C | 77 | Sb06g024943 |
| CSt_Anth_W−1 | S6_54057566 | 0.002 | −19.29 | G/C | (+)2144 | Sb06g025060 |
| CSt_Anth_W−1 | S6_53978420 | 0.022 | −20.33 | G/C | 661 | Sb06g024960 |
| CSt_Anth_W−1 | S6_54030245 | 0.017 | −13.36 | G/A | (−)440 | Sb06g025040 |
| CSt_Anth_W−1 | S6_53848121 | 0.023 | −5.18 | T/C | (+)4385 | Sb06g024820 |
| CSt_Anth_W−1 | S6_53791123 | 0.019 | 5.21 | T/C | (+)2883 | Sb06g024740 |
| CSt_Anth_W−1 | S6_43169342 | 0.023 | −47.53 | A/G | 108 | Sb06g015560 |
| CSt_Anth_W−1 | S6_54030254 | 0.017 | 13.36 | G/T | (−)449 | Sb06g025040 |
| CSt_Anth_W−1 | S2_76203986 | 0.025 | 36.77 | C/T | (−)2259 | Sb02g042450 |
*False Discovery Rate (FDR) values for the significantly associated SNP at p-value of 1E-06
**Percent trait variation explained by the associated SNPs
***Distance to the nearest annotated gene coordinates in the reference genome