Table 1 List of significant SNP markers (qualified Bonferroni criteria) associated with yield and its related traits, desirable allele and SNP effects.
Trait | Environment | SNP | Clone ID | Chromosome | Position (cM) | SNP alleles | Desirable allele | −log (p) | SNP effect |
|---|---|---|---|---|---|---|---|---|---|
DTH | E1, E2 | SNP_404 | 1103347 | 1A | 247.886 | G/T | G | 8.5–8.1 | 3.7 to 4.7 |
E1 | SNP_647 | 1096003 | 1B | 64.812 | G/T | G | 7.1 | 4.9 | |
E1, E2 | SNP_5304 | 1003062 | 4B | 60.121 | T/G | G | 8.3–6.7 | −4.1 to −4.3 | |
E2 | SNP_2860 | 1026541 | 2B | 179.515 | C/G | C | 9.3 | 4.5 | |
E2 | SNP_7937 | 1129498 | 6D | 9.626 | T/C | T | 8.0 | 2 | |
E2 | SNP_6361 | 1050557 | 5B | 85.982 | G/C | C | 6.4 | −2.7 | |
E2 | SNP_3398 | 1063624 | 3A | 75.969 | G/T | G | 6.1 | 3.4 | |
E3 | SNP_1204 | 986158 | 1B | 384.128 | A/T | A | 10.2 | 2.7 | |
E3 | SNP_5593 | 1110448 | 4D | 123.880 | G/T | T | 7.7 | −4.0 | |
E3 | SNP_5815 | 1133812 | 5A | 96.128 | C/G | C | 6.6 | 1.8 | |
E3, E4 | SNP_4482 | 1069547 | 3B | 253.745 | C/A | C | 12.1–6.2 | 2.0 to 2.9 | |
E3 | SNP_4509 | 1134753 | 3B | 264.027 | C/G | G | 6.1 | −1.9 | |
E4 | SNP_6544 | 3023142 | 5B | 171.943 | G/C | C | 7.6 | −2.6 | |
E4 | SNP_2075 | 1083327 | 2A | 237.185 | G/C | G | 7.5 | 2.2 | |
DTM | E1, E2, E4 | SNP_404 | 1103347 | 1A | 247.886 | G/T | G | 9.4–6.7 | 3.0 to 3.9 |
E1, E2 | SNP_5304 | 1003062 | 4B | 60.121 | T/G | G | 6.4–6.1 | −3.2 to −3.3 | |
E1, E2 | SNP_3398 | 1063624 | 3A | 75.969 | G/T | G | 6.2–6.1 | 3.6 to 3.7 | |
E2 | SNP_1302 | 100001553 | 1B | 520.423 | T/C | C | 7.3 | −3.1 | |
E2 | SNP_647 | 1096003 | 1B | 64.812 | G/T | G | 7.0 | 3.8 | |
E3 | SNP_5369 | 1270494 | 4B | 76.346 | T/C | C | 8.1 | −2.7 | |
E3 | SNP_9088 | 992291 | 7B | 114.753 | C/T | C | 7.7 | 1.4 | |
E3 | SNP_2054 | 1125402 | 2A | 231.786 | C/G | G | 7.0 | −3.1 | |
E3 | SNP_7797 | 1093068 | 6B | 82.603 | C/T | T | 6.5 | −1.7 | |
E3 | SNP_7068 | 1073429 | 6A | 88.944 | C/T | C | 6.1 | 2.2 | |
E4 | SNP_2003 | 1021420 | 2A | 224.605 | G/A | A | 8.7 | −2.2 | |
PH | E2 | SNP_5988 | 1090844 | 5A | 177.183 | G/C | C | 7.5 | −3.0 |
E3 | SNP_5396 | 3028936 | 4B | 80.804 | C/T | C | 6.5 | 4.0 | |
E3 | SNP_7799 | 1080969 | 6B | 83.710 | C/G | C | 6.1 | 3.8 | |
E4 | SNP_4022 | 1127414 | 3B | 94.818 | A/G | G | 7.6 | −3.4 | |
E4 | SNP_693 | 1113894 | 1B | 91.804 | T/G | G | 6.8 | −4.6 | |
TGW | E1, E2 | SNP_7068 | 1073429 | 6A | 88.944 | C/T | C | 7.9–6.2 | −2.1 to −2.8 |
E1 | SNP_7775 | 1026425 | 6B | 75.404 | G/C | G | 6.0 | −2.4 | |
E2 | SNP_5008 | 1094628 | 4A | 177.335 | T/G | G | 8.3 | 1.5 | |
E2 | SNP_6346 | 1167608 | 5B | 79.052 | G/T | T | 7.8 | 1.5 | |
E2 | SNP_5294 | 985312 | 4B | 57.883 | G/A | G | 7.7 | −1.5 | |
E2 | SNP_3294 | 3030495 | 3A | 21.260 | A/G | A | 6.5 | −1.7 | |
E2 | SNP_3179 | 1228079 | 2D | 289.675 | T/C | T | 6.4 | −2.1 | |
E3 | SNP_7797 | 1093068 | 6B | 82.603 | C/T | T | 6.2 | 2.1 | |
E4 | SNP_1829 | 977937 | 2A | 150.126 | G/A | G | 6.9 | −1.8 | |
E4 | SNP_3449 | 1065193 | 3A | 88.133 | T/C | T | 6.9 | −1.8 | |
GYPP | E1 | SNP_5249 | 1126379 | 4A | 250.448 | T/A | T | 7.0 | −29.3 |
E1 | SNP_7747 | 985813 | 6B | 69.052 | C/A | C | 6.9 | −33.7 | |
E1 | SNP_8465 | 1093542 | 7A | 157.225 | A/G | A | 6.6 | −29.3 | |
E3 | SNP_6795 | 1091457 | 5D | 100.955 | A/G | G | 8.2 | 32.3 | |
E3 | SNP_4163 | 1202201 | 3B | 117.678 | G/A | A | 7.1 | 26.9 | |
E3 | SNP_2974 | 1217183 | 2B | 203.502 | A/G | A | 6.1 | −22.1 |
