Table 1 Significant loci associated with pork cuts and carcass morphology traits by haplotypes-based GWAS
From: Genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig
Traits | Top SNP | Chr | Pos, bp | P-value | Candidate gene1 | Dis2, bp |
|---|---|---|---|---|---|---|
Pork cuts weight | ||||||
 Ribs | rs0702042 | 7 | 97,732,109 | 8.41E-13 | VRTN | 107,836 |
 Back fat | rs0103099 | 1 | 161,408,832 | 6.30E-07 | CCBE1 | Within |
 Hind leg bones | rs1705050 | 17 | 15,949,323 | 6.25E-11 | BMP2 | 188,108 |
 Leg cut | rs0501529 | 5 | 81,315,221 | 9.35E-07 | IGF1 | 460,749 |
Pork cuts proportion | ||||||
 Boneless boston shoulder | rs0701491 | 7 | 65,738,048 | 7.89E-07 | EGLN3 | 67,452 |
 Fore leg bones | rs0700815 | 7 | 31,161,760 | 4.03E-09 | HMGA1 | 832,351 |
 Fore leg bones | rs0901869 | 9 | 84,593,678 | 8.43E-07 | AGMO | Within |
 Ribs | rs0702042 | 7 | 97,732,109 | 1.05E-16 | VRTN | 107,836 |
 Back fat | rs0103099 | 1 | 161,408,832 | 1.57E-07 | CCBE1 | Within |
 Middle cut | rs0702038 | 7 | 97,618,073 | 1.70E-11 | VRTN | Within |
 Middle cut | rs0700525 | 7 | 19,581,991 | 8.72E-07 | GMNN | 4008 |
 Hind leg bones | rs1705090 | 17 | 17,801,643 | 5.32E-08 | BMP2 | 2,040,428 |
Carcass morphology traits | ||||||
 Straight length | rs1705043 | 17 | 15,562,883 | 2.00E-17 | VRTN | Within |
 Straight length | rs0702038 | 7 | 97,618,073 | 1.04E-14 | BMP2 | 186,952 |
 Straight length | rs1704946 | 17 | 9,342,605 | 8.71E-07 | IDO2 | Within |
 Oblique length | rs0702038 | 7 | 97,618,073 | 2.57E-14 | VRTN | Within |
 Oblique length | rs1705050 | 17 | 15,949,323 | 4.59E-12 | BMP2 | 188,108 |
 Thoracic number | rs0702038 | 7 | 97,618,073 | 6.70E-169 | VRTN | Within |
 Thoracic number | rs0701070 | 7 | 42,952,142 | 3.58E-07 | PTCHD4 | 182,162 |
 Thoracic length | rs0702038 | 7 | 97,618,073 | 8.16E-60 | VRTN | Within |
 Thoracic length | rs1302182 | 13 | 103,068,791 | 2.01E-07 | TMEM266 | Within |
 Thoracic length | rs1303285 | 13 | 159,490,799 | 3.01E-07 | SI | 1,227,492 |
 Thoracic length | rs0701325 | 7 | 56,379,471 | 4.48E-07 | COL8A1 | 116,295 |
 Thoracic length | rs1705043 | 17 | 15,562,883 | 7.04E-07 | BMP2 | 186,952 |
 Lumbar length | rs0702035 | 7 | 97,347,282 | 5.84E-07 | VRTN | 267,425 |
 Single lumbar length | rs0101891 | 1 | 88,605,020 | 9.40E-07 | HTR1B | 3,973 |