Table 3.
Information for all significant SNP related to body size and carcass traits
| Trait | Nbsnp | Chr | Position (ps) | AF | Beta | p-value | Var (%) | Candidate gene | Distance |
|---|---|---|---|---|---|---|---|---|---|
| BMW | 2 | 3 | 11,176,648 | 0.276 | −2.55E-01 | 2.53E-05 | 4.1 | TMEM17 | 7442 bp upstream |
| 10 | 1,656,050 | 0.366 | −2.35E-01 | 2.96E-05 | 4.1 | LOC101804888 | 11,627 bp downstream | ||
| BMWP | 3 | 1 | 867,910 | 0.45 | 2.56E-01 | 3.18E-06 | 8.1 | LOC101803092 | within |
| 1 | 47,950,429 | 0.397 | −2.39E-01 | 6.71E-06 | 6.9 | ATP2B1 | 107,815 bp upstream | ||
| 1 | 47,950,615 | 0.402 | −2.31E-01 | 1.82E-05 | 6.4 | ATP2B1 | 107,629 bp upstream | ||
| BrW | 4 | 2 | 19,666,206 | 0.479 | −2.39E-01 | 1.45E-05 | 9.8 | PLXDC2 | 5029 bp downstream |
| 2 | 24,791,499 | 0.362 | −2.60E-01 | 7.69E-06 | 10.8 | LOC101799835 | within | ||
| 6 | 31,223,243 | 0.369 | 2.22E-01 | 2.14E-05 | 7.9 | WDR11 | 29,320 bp upstream | ||
| 21 | 1,548,509 | 0.427 | 2.31E-01 | 2.59E-05 | 9 | EYA2 | 28,420 bp downstream | ||
| BW42 | 5 | 1 | 85,234,035 | 0.455 | −2.29E-01 | 1.12E-05 | 4.1 | LOC101789880 | within |
| 1 | 140,105,435 | 0.305 | −2.64E-01 | 1.20E-07 | 4.6 | ATP11A | within | ||
| 1 | 140,105,568 | 0.47 | 2.16E-01 | 6.54E-06 | 3.6 | ATP11A | within | ||
| 2 | 19,666,336 | 0.229 | −2.29E-01 | 2.25E-05 | 2.9 | PLXDC2 | 5159 bp downstream | ||
| 28 | 3,372,077 | 0.024 | −6.23E-01 | 3.16E-05 | 2.8 | LOC101803004 | 1892 bp downstream | ||
| DP | 2 | 1 | 7,468,875 | 0.358 | 2.22E-01 | 1.07E-05 | 4.9 | GRM3 | 121,336 bp downstream |
| 6 | 33,060,881 | 0.368 | 2.35E-01 | 3.09E-06 | 5.6 | CTBP2 | 30,880 bp downstream | ||
| DW | 8 | 1 | 63,206,125 | 0.395 | −2.41E-01 | 1.75E-05 | 4.6 | CACNA1C | within |
| 1 | 85,234,035 | 0.455 | −2.28E-01 | 7.68E-06 | 4.3 | LOC101789880 | within | ||
| 1 | 140,105,435 | 0.305 | −2.55E-01 | 1.65E-07 | 4.6 | ATP11A | within | ||
| 1 | 140,105,568 | 0.47 | 2.06E-01 | 9.97E-06 | 3.5 | ATP11A | within | ||
| 1 | 141,660,288 | 0.44 | 2.05E-01 | 1.72E-05 | 3.4 | LOC101802568 | 26,100 bp downstream | ||
| 1 | 158,535,990 | 0.35 | −2.14E-01 | 1.54E-05 | 3.5 | KLF5 | 44,712 bp upstream | ||
| 2 | 19,666,336 | 0.229 | −2.40E-01 | 5.01E-06 | 3.4 | PLXDC2 | 5159 bp downstream | ||
| 28 | 3,372,077 | 0.024 | −6.41E-01 | 1.46E-05 | 3.2 | LOC101803004 | 1892 bp downstream | ||
| EW | 6 | 1 | 63,206,125 | 0.395 | −2.47E-01 | 1.51E-05 | 5 | CACNA1C | within |
| 1 | 140,105,435 | 0.305 | −2.65E-01 | 1.02E-07 | 5.1 | ATP11A | within | ||
| 1 | 140,105,568 | 0.47 | 2.02E-01 | 2.52E-05 | 3.5 | ATP11A | within | ||
| 1 | 158,535,990 | 0.35 | −2.22E-01 | 1.15E-05 | 3.9 | KLF5 | 44,712 bp upstream | ||
| 2 | 19,666,336 | 0.229 | −2.32E-01 | 1.65E-05 | 3.3 | PLXDC2 | 5159 bp downstream | ||
| 28 | 3,372,077 | 0.024 | −6.37E-01 | 2.02E-05 | 3.3 | LOC101803004 | 1892 bp downstream | ||
| EWP | 4 | 2 | 35,813,875 | 0.372 | −2.27E-01 | 2.74E-05 | 5.5 | CHN2 | within |
| 3 | 89,970,339 | 0.313 | −2.24E-01 | 2.59E-05 | 4.9 | LGSN | 57,852 bp downstream | ||
| 13 | 17,512,359 | 0.391 | −2.18E-01 | 1.02E-05 | 5.1 | FOXP1 | 2160 bp downstream | ||
| 18 | 5,703,171 | 0.433 | 2.29E-01 | 8.74E-06 | 5.8 | PPP1R26 | 37,536 bp upstream | ||
| FBL | 3 | 2 | 40,157,075 | 0.49 | 2.44E-01 | 1.50E-05 | 6.6 | OXSM | 15,327 bp downstream |
| 2 | 52,398,515 | 0.419 | 2.40E-01 | 1.13E-05 | 6.2 | TNS3 | within | ||
| 2 | 137,295,017 | 0.372 | −2.18E-01 | 3.17E-05 | 5 | TMEM74 | 1377 bp upstream | ||
| FW | 2 | 1 | 148,339,868 | 0.018 | 7.08E-01 | 7.73E-06 | 3.2 | ABCC4 | within |
| 4 | 59,568,289 | 0.02 | 6.09E-01 | 1.62E-05 | 2.6 | LDB2 | 17,964 bp downstream | ||
| HEW | 6 | 1 | 63,206,125 | 0.395 | −2.46E-01 | 1.85E-05 | 5 | CACNA1C | within |
| 1 | 140,105,435 | 0.305 | −2.72E-01 | 5.27E-08 | 5.4 | ATP11A | within | ||
| 1 | 140,105,568 | 0.47 | 2.06E-01 | 1.98E-05 | 3.6 | ATP11A | within | ||
| 1 | 158,535,990 | 0.35 | −2.24E-01 | 1.02E-05 | 3.9 | KLF5 | 44,712 bp upstream | ||
| 2 | 19,666,336 | 0.229 | −2.35E-01 | 1.38E-05 | 3.4 | PLXDC2 | 5159 bp downstream | ||
| 28 | 3,372,077 | 0.024 | −6.28E-01 | 2.95E-05 | 3.2 | LOC101803004 | 1892 bp downstream | ||
| HEWP | 2 | 1 | 196,705,092 | 0.357 | 2.18E-01 | 2.95E-05 | 5.1 | LOC101797437 | 5799 bp downstream |
| 13 | 17,512,359 | 0.391 | −2.12E-01 | 2.27E-05 | 5 | FOXP1 | 2160 bp downstream | ||
| HW | 4 | 1 | 158,535,990 | 0.35 | −2.53E-01 | 2.06E-06 | 8.6 | KLF5 | 44,712 bp upstream |
| 3 | 64,428,149 | 0.434 | 2.29E-01 | 8.58E-06 | 7.6 | GJA1 | 14,583 bp downstream | ||
| 5 | 22,865,850 | 0.351 | 2.30E-01 | 6.43E-06 | 7.1 | AQR | 11,077 bp upstream | ||
| 7 | 11,397,351 | 0.312 | −2.35E-01 | 2.62E-05 | 7 | PCNT | within | ||
| LW | 5 | 1 | 119,976,059 | 0.407 | −2.12E-01 | 1.31E-05 | 3.6 | LOC101803212 | 13,772 bp downstream |
| 1 | 34,185,127 | 0.242 | −2.24E-01 | 2.47E-05 | 3.1 | PPM1H | within | ||
| 4 | 427,963 | 0.473 | 2.19E-01 | 9.55E-06 | 4 | LOC101798797 | 148,591 bp downstream | ||
| 4 | 59,555,379 | 0.016 | 6.79E-01 | 3.37E-05 | 2.4 | LDB2 | 4954 bp downstream | ||
| 8 | 23,698,948 | 0.419 | 2.21E-01 | 2.95E-05 | 4 | AGBL4 | within | ||
| LMWP | 1 | 20 | 2,198,171 | 0.385 | −2.40E-01 | 2.73E-05 | 3 | AUTS2 | 30,531 bp downstream |
| NL | 1 | 1 | 130,709,943 | 0.354 | −2.01E-01 | 2.79E-05 | 4.4 | XG | within |
| WW | 2 | 1 | 140,105,435 | 0.305 | −2.44E-01 | 6.49E-07 | 4.4 | ATP11A | within |
| 2 | 149,672,484 | 0.015 | 8.53E-01 | 2.67E-05 | 3.8 | FAM135B | 33,375 bp downstream |
Neck length (NL), Fossil bone length (FBL), Breast width (BrW), Dressed weight (DW), Dressed percentage (DP), Eviscerated weight (EW), Eviscerated weight percentage (EWP), Half-eviscerated weight (HEW), Percentage of half-eviscerated yield (HEWP), 42-day body weight (BW42), Heart weight (HW), Liver weight (LW), Foot weight (FW), Wing weight (WW), Breast muscle weight (BMW), Breast muscle weight percentage (BMWP), Leg muscle weight (LMW), Leg muscle weight percentage (LMWP). Chr, chromosomeID; Nbsnp, number of significant SNP, retaining the most significant one if the distance between multiple SNP of the same trait is less than 0.15 Mb; AF, minor allele frequency; Beta, the estimate coefficient; Var (%), % of genetic variance explained by the top SNP