Table 2.
List of significant MTAs along with contrasting alleles, chromosome, position, minor allele frequency (MAF) and SNP effect. 0.001 is considered as P-value cut off for significant MTAs. Earlier studies where QTLs are reported for same trait on same chromosomes are mentioned in last column.
| Trait | SNP | Alleles | Chromosome | Position | −log(p) | MAF | SNP effect | References |
|---|---|---|---|---|---|---|---|---|
| DOF | C2.27561819 | A/G | 2 | 27561819 | 3.5 | 0.29 | 1.99 | 25, 42 |
| FLL | C2.27562491 | A/T | 2 | 27562491 | 3.7 | 0.14 | 2.89 | 17, 42 |
| C2.27562638 | A/C | 2 | 27562638 | 3.7 | 0.14 | 2.89 | ||
| C2.27726456 | G/A | 2 | 27726456 | 3.1 | 0.27 | 2.11 | ||
| C5.17545821 | C/G | 5 | 17545821 | 3.1 | 0.11 | 3.25 | 17 | |
| C5.17545822 | A/C | 5 | 17545822 | 3.1 | 0.11 | 3.25 | ||
| C5.20371666 | C/A | 5 | 20371666 | 3.1 | 0.11 | 3.25 | ||
| C5.20537816 | G/A | 5 | 20537816 | 3.4 | 0.11 | 3.38 | ||
| FLW | C1.6814673 | T/C | 1 | 6814673 | 4.7 | 0.13 | −0.5 | — |
| C1.6814709 | A/G | 1 | 6814709 | 4.7 | 0.13 | −0.5 | ||
| C1.6814725 | A/G | 1 | 6814725 | 4.7 | 0.13 | −0.5 | ||
| C1.6825210 | T/C | 1 | 6825210 | 5.1 | 0.11 | −0.41 | ||
| C1.6898417 | G/T | 1 | 6898417 | 5.5 | 0.15 | 0.13 | ||
| C1.6904134 | A/G | 1 | 6904134 | 3.1 | 0.12 | −0.35 | ||
| C2.45151497 | G/A | 2 | 45151497 | 4.5 | 0.3 | 0.13 | 17, 42 | |
| C3.30858639 | G/A | 3 | 30858639 | 4.6 | 0.06 | −0.25 | — | |
| C4.17271685 | C/G | 4 | 17271685 | 3.2 | 0.11 | −0.2 | — | |
| C4.17271782 | C/T | 4 | 17271782 | 3.2 | 0.11 | −0.19 | ||
| C4.17271815 | A/G | 4 | 17271815 | 3.2 | 0.11 | −0.2 | ||
| C6.2639715 | G/C | 6 | 2639715 | 3.2 | 0.11 | 0.13 | — | |
| C7.26457626 | G/A | 7 | 26457626 | 3.4 | 0.24 | −0.13 | 25 | |
| C7.34109248 | A/C | 7 | 34109248 | 5.7 | 0.07 | 0.31 | ||
| C8.29396204 | C/T | 8 | 29396204 | 5.4 | 0.06 | −0.3 | — | |
| C8.29469536 | G/A | 8 | 29469536 | 5.6 | 0.06 | 0.37 | ||
| C9.37225457 | C/T | 9 | 37225457 | 17.3 | 0.12 | 0.16 | — | |
| C9.37443288 | C/A | 9 | 37443288 | 16.5 | 0.11 | −1.84 | ||
| C9.37523364 | C/A | 9 | 37523364 | 6.0 | 0.12 | −0.68 | ||
| C9.38068016 | C/T | 9 | 38068016 | 16.5 | 0.11 | −1.84 | ||
| C9.47023159 | A/T | 9 | 47023159 | 4.6 | 0.09 | 0.19 | ||
| GY | C1.19584662 | A/G | 1 | 19584662 | 4.2 | 0.11 | 2.26 | — |
| C1.31690904 | G/A | 1 | 31690904 | 4.6 | 0.1 | −3 | ||
| C2.2290737 | A/T | 2 | 2290737 | 3.9 | 0.09 | 2.43 | — | |
| C3.27957942 | G/A | 3 | 27957942 | 3.1 | 0.07 | −2.48 | 25 | |
| C3.28147097 | G/A | 3 | 28147097 | 3.1 | 0.07 | −2.48 | ||
| C3.29268216 | T/A | 3 | 29268216 | 3.1 | 0.07 | −2.48 | ||
| C3.32214003 | G/C | 3 | 32214003 | 3.1 | 0.07 | −2.48 | ||
| C3.32823330 | C/T | 3 | 32823330 | 3.1 | 0.07 | −2.48 | ||
| C3.35621706 | C/T | 3 | 35621706 | 3.4 | 0.08 | −2.51 | ||
| C3.50114070 | A/G | 3 | 50114070 | 6.8 | 0.07 | 4.05 | ||
| C3.50516216 | T/C | 3 | 50516216 | 3.2 | 0.38 | −1.34 | ||
| C5.3047617 | C/G | 5 | 3047617 | 4.7 | 0.07 | 2.7 | — | |
| C6.2476369 | C/T | 6 | 2476369 | 3.5 | 0.2 | −1.47 | — | |
| C7.12591441 | G/A | 7 | 12591441 | 4.3 | 0.11 | 2.89 | — | |
| C7.14255739 | C/T | 7 | 14255739 | 3.4 | 0.15 | −1.73 | ||
| C7.19705515 | A/C | 7 | 19705515 | 6.1 | 0.13 | 6.18 | ||
| C8.33295392 | C/G | 8 | 33295392 | 4.6 | 0.37 | 1.34 | — | |
| PanL | C2.29645716 | G/A | 2 | 29645716 | 3.4 | 0.22 | 1.57 | 17, 58 |
| C2.29645949 | T/C | 2 | 29645949 | 3.8 | 0.23 | 1.62 | ||
| C3.14502439 | C/T | 3 | 14502439 | 3.0 | 0.39 | −1.25 | 25 | |
| C5.13976998 | C/A | 5 | 13976998 | 3.1 | 0.09 | 3.23 | 17 | |
| C7.3618032 | T/C | 7 | 3618032 | 3.3 | 0.11 | −2.07 | 25 | |
| C8.4806303 | T/C | 8 | 4806303 | 3.3 | 0.11 | −1.86 | 25, 59 | |
| C9.54570214 | G/T | 9 | 54570214 | 3.2 | 0.12 | 1.83 | 17, 25 | |
| PedL | C9.14370304 | A/C | 9 | 14370304 | 4.1 | 0.13 | 2.11 | — |
| C9.54646405 | C/A | 9 | 54646405 | 3.5 | 0.19 | 1.74 | ||
| PH | C5.9294227 | C/G | 5 | 9294227 | 3.4 | 0.24 | 9.02 | 17, 42 |
| C5.17368448 | G/C | 5 | 17368448 | 3.0 | 0.12 | 11.32 | ||
| C7.13010170 | A/C | 7 | 13010170 | 3.1 | 0.07 | 13.73 | 17, 58 | |
| TGW | C2.1884254 | G/A | 2 | 1884254 | 4.8 | 0.21 | 0.14 | — |
| C2.4114681 | T/C | 2 | 4114681 | 4.5 | 0.32 | 0.1 | ||
| C3.4813917 | T/C | 3 | 4813917 | 3.7 | 0.23 | 0.1 | 17, 25 | |
| C3.43310250 | C/T | 3 | 43310250 | 4.9 | 0.06 | −0.25 | ||
| C6.34654923 | T/C | 6 | 34654923 | 7.0 | 0.13 | −0.21 | 25 | |
| C8.23236893 | C/A | 8 | 23236893 | 3.0 | 0.07 | 0.13 | — | |
| C8.34760860 | A/C | 8 | 34760860 | 4.2 | 0.36 | 0.1 | ||
| C8.39522974 | C/T | 8 | 39522974 | 3.7 | 0.25 | 0.11 | ||
| C9.37011889 | A/G | 9 | 37011889 | 8.3 | 0.08 | −0.33 | 59 | |
| C9.55718390 | T/G | 9 | 55718390 | 3.7 | 0.1 | −0.19 | ||
| TM | C3.50460866 | T/C | 3 | 50460866 | 3.7 | 0.37 | 2.88 | — |
| C5.6559967 | G/A | 5 | 6559967 | 3.0 | 0.13 | −3.5 | — | |
| C6.34314915 | G/A | 6 | 34314915 | 3.5 | 0.41 | 2.58 | — | |
| C7.18807581 | A/G | 7 | 18807581 | 3.2 | 0.06 | −4.82 | — | |
| C7.18869945 | G/C | 7 | 18869945 | 3.3 | 0.06 | −4.88 | ||
| C8.2541016 | G/C | 8 | 2541016 | 3.2 | 0.16 | −3.33 | — | |
| C9.10635590 | T/C | 9 | 10635590 | 3.2 | 0.2 | 3.02 | — | |
| TN | C4.8882993 | G/A | 4 | 8882993 | 3.1 | 0.22 | 0.49 | 17, 25 |
| C7.19587543 | G/A | 7 | 19587543 | 3.2 | 0.13 | 0.98 | 25 | |
| C7.19696191 | C/T | 7 | 19696191 | 3.3 | 0.11 | 1.29 | ||
| C7.19705515 | A/C | 7 | 19705515 | 3.6 | 0.13 | 1.37 | ||
| C7.19718741 | G/A | 7 | 19718741 | 3.3 | 0.11 | 1.29 | ||
| C9.37523364 | C/A | 9 | 37523364 | 3.1 | 0.12 | 0.91 | 25 |