Table 3.
Description of SNPs significantly associated with meat quality traits in Erhualian and DLY pigs
| Traits 2 | Peak SNP | No. 3 | Chr | Pos (bp) 4 | PPL 5 | Nearest genes 6 | Freq 7 | Effects 8 | P -value 9 |
|---|---|---|---|---|---|---|---|---|---|
| EHL 1 | |||||||||
| LM_pH24h | ss131409440 | 1 | 9 | 144 399 17 | INTS7 | 0.67 | 0.088 | 9.78E-06 | |
| SM_pH24h | ss131225834 | 1 | 3 | 15 271 92 | WBSCR17 | 0.33 | 0.185 | 3.13E-06 | |
| LM_pHdrop_45min-24 h | ss107857062 | 1 | 16 | 79 490 30 | c | SEMA5A | 0.53 | 0.158 | 8.05E-06 |
| LM_DripEZ_24h | ss131261254 | 1 | 4 | 44 336 60 | ENSSSCG00000019169 | 0.15 | 0.686 | 7.97E-09 | |
| LM_DripEZ_24h | ss478940762 | 2 | 4 | 35 761 053 | RIMS2 | 0.12 | 0.618 | 2.62E-06 | |
| LM_DripEZ_24h | ss131270350 | 1 | 4 | 85 151 430 | ST18 | 0.14 | 1.092 | 6.26E-06 | |
| SM_DripEZ_24h | ss131134976 | 1 | 1 | 181 797 733 | MEGF11 | 0.50 | 0.247 | 2.31E-06 | |
| LM_ColorM_a24h | ss131341943 | 1 | 7 | 31 500 144 | KLHL31 | 0.60 | 0.505 | 9.1E-06 | |
| LM_ColorM_a24h | ss478937995 | 3 | 12 | 58 130 567 | b | MYH3 | 0.18 | 0.945 | 1.04E-05 |
| LM_ColorM_a24h | ss131565824 | 1 | 5 | 2 588 817 | EFCAB6 | 0.65 | 0.545 | 1.18E-05 | |
| LM_ColorM_b24h | ss120027962 | 1 | 14 | 11 463 494 | BNIP3L | 0.02 | 1.628 | 3.64E-06 | |
| LM_ColorM_b24h | ss478937995 | 2 | 12 | 58 130 567 | b | MYH3 | 0.18 | 0.976 | 1.65E-05 |
| LM_ColorScore_24h | ss131352394 | 1 | 7 | 5 406 955 | a | EEF1E1 | 0.74 | 0.234 | 5.49E-06 |
| LM_ColorScore_24h | ss131461879 | 1 | 12 | 36 158 023 | SUPT4H1 | 0.63 | 0.208 | 2.29E-05 | |
| SM_ColorM_b24h | ss107878019 | 1 | 12 | 9 939 154 | ENSSSCG00000025361 | 0.95 | 1.435 | 1.88E-05 | |
| SM_ColorScore_24h | ss478943784 | 1 | 17 | 56 358 556 | SULF2 | 0.33 | 0.235 | 7.70E-06 | |
| LM_MoistureContent | ss131186989 | 1 | 2 | 43 911 957 | LDHA | 0.01 | 1.010 | 5.18E-06 | |
| LM_MoistureContent | ss131458048 | 1 | 12 | 24 427 829 | NFE2L1 | 0.01 | 0.860 | 5.31E-06 | |
| LM_MoistureContent | ss131054125 | 1 | 8 | 14 014 229 | ENSSSCG00000029791 | 0.51 | 0.653 | 8.07E-06 | |
| LM_MoistureContent | ss131538960 | 2 | 16 | 74 982 852 | c | MFAP3 | 0.86 | 1.112 | 1.67E-05 |
| LM_Firmness | ss131096544 | 2 | 12 | 57 123 997 | b | WDR16 | 0.72 | 0.232 | 4.10E-06 |
| LM_Firmness | ss478937524 | 1 | 7 | 7 764 396 | a | TMEM14C | 0.64 | 0.225 | 1.81E-05 |
| DLY 1 | |||||||||
| LM_DripEZ_36h | ss131494523 | 1 | 13 | 141 530 003 | FAM43A | 0.36 | 0.435 | 1.53E-05 | |
| LM_DripEZ_36h | ss131400253 | 1 | 9 | 95 957 104 | d | SNX13 | 0.88 | 0.740 | 1.57E-05 |
| LM_ColorM_a36h | ss107833468 | 1 | 15 | 134 397 712 | e | RESP18 | 0.37 | 0.245 | 1.78E-05 |
| LM_ColorM_b36h | ss107856037 | 1 | 15 | 92 671 886 | AGPS | 0.32 | 0.569 | 9.17E-06 | |
| LM_ColorScore_36h | ss131398982 | 1 | 9 | 84 832 035 | d | ASNS | 0.62 | 0.122 | 4.78E-06 |
| LM_ColorScore_36h | ss131528409 | 1 | 15 | 127 419 860 | e | IKZF2 | 0.56 | 0.153 | 7.27E-06 |
| LM_ColorScore_36h | ss107897208 | 1 | 9 | 45 577 347 | NCAM1 | 0.44 | 0.148 | 9.96E-06 | |
| LM_ColorScore_36h | ss107799219 | 1 | 0 | 0 | 0.98 | 0.543 | 1.46E-05 | ||
| LM_Firmness | ss131184920 | 1 | 2 | 34 977 540 | KIF18A | 0.37 | 0.172 | 1.47E-05 |
1Chinese Erhualian indigenous population and Western Duroc × (Landrace × Yorkshire) commercial population; 2description of the traits is in Table 1; 3number of SNPs that surpassed the suggestive significance level within the QTL regions; 4positions of the most significant SNP according to the Sus Scrofa Build 10.2 assembly; 5possible pleiotropic loci (PPL) were indicated by common letters on different rows; 6annotated genes nearest to the most significant SNP; gene names starting with ENSSSCG follow the Ensembl nomenclature while other gene symbols follow the HUGO nomenclature; 7,8frequencies and effects of the allele that increases phenotype value in the two populations; 9genome-wide significant associations are underlined.