Table 3.
(a) The genome-level significant SNPs and possible candidate genes for carcass traits. (b) The genome-level significant SNPs and possible candidate genes for meat quality traits.
| (a) | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Trait | SNP (Rsid) | CHR | POS (bp) | Consequence | MAF | PVE (%) | P-adj | Nearest Gene | DIS (bp) |
| CL | ALGA0040227 (rs80983858) |
7 | 30,176,520 | Downstream gene variant | 0.39 | 14.35 | 8.05 × 10−19 | GRM4 | 2785 |
| ALGA0040238 (rs80815545) |
7 | 30,197,014 | Intron variant | 0.36 | 12.98 | 4.72 × 10−11 | GRM4 | Within | |
| INRA0024788 (–––) |
7 | 30,31,7219 | ––– | 0.36 | 10.08 | 2.16 × 10−13 | HMGA1 | 3191 | |
| ALGA0039917 (rs81397589) |
7 | 26,737,102 | Intron variant | 0.19 | 7.02 | 1.25 × 10−9 | MLIP | Within | |
| ALGA0040777 (rs80845178) |
7 | 36,323,988 | Intergenic variant | 0.44 | 6.28 | 9.85 × 10−9 | UNC5CL | 8213 | |
| ALGA0040243 (rs80942143) |
7 | 30,213,771 | Intron variant | 0.25 | 5.69 | 4.97 × 10−8 | GRM4 | Within | |
| WU_10.2_7_48537179 (–––) |
7 | 41,877,149 | ––– | 0.42 | 5.66 | 5.39 × 10−8 | ADGRF1 | 23,492 | |
| ASGA0032589 (rs80869188) |
7 | 31,450,019 | Intron variant | 0.32 | 5.13 | 2.36 × 10−7 | FKBP5 | Within | |
| H3GA0020641 (rs80975871) |
7 | 28,521,421 | Intron variant | 0.11 | 4.92 | 4.17 × 10−7 | PRIM2 | Within | |
| ALGA0039880 (rs80928470) |
7 | 26,501,975 | Intron variant | 0.11 | 4.86 | 5.04 × 10−7 | TINAG | Within | |
| ALGA0041948 (rs80997002) |
7 | 50,283,279 | Intergenic variant | 0.47 | 4.77 | 6.30 × 10−7 | TMC3 | 99,190 | |
| ALGA0040370 (rs81397836) |
7 | 32,328,188 | Intergenic variant | 0.48 | 4.60 | 1.02 × 10−6 | SRSF3 | 29,608 | |
| M1GA0010006 (rs80946246) |
7 | 31,161,760 | Intron variant | 0.31 | 4.55 | 1.16 × 10−6 | ZNF76 | Within | |
| WU_10.2_7_36255497 (–––) |
7 | 31,181,718 | –––– | 0.31 | 4.55 | 1.16 × 10−6 | ZNF76 | Within | |
| MARC0060950 (rs80924014) |
7 | 46,569,153 | Upstream gene variant | 0.16 | 4.44 | 1.58 × 10−6 | TMEM14A | 51,421 | |
| COL | ALGA0040227 (rs80983858) |
7 | 30,176,520 | Downstream gene variant | 0.39 | 8.38 | 2.67 × 10−25 | GRM4 | 2785 |
| ALGA0040238 (rs80815545) |
7 | 30,197,014 | Intron variant | 0.36 | 7.51 | 3.17 × 10−10 | GRM4 | Within | |
| ALGA0039880 (rs80928470) |
7 | 26,501,975 | Intron variant | 0.11 | 5.75 | 4.19 × 10−7 | TINAG | Within | |
| H3GA0020641 (rs80975871) |
7 | 28,521,421 | Intron variant | 0.11 | 5.14 | 2.30 × 10−7 | PRIM2 | Within | |
| ALGA0039917 (rs81397589) |
7 | 26,737,102 | Intron variant | 0.19 | 4.88 | 4.74 × 10−7 | MLIP | Within | |
| INRA0024788 | 7 | 30,317,219 | ––– | 0.36 | 4.63 | 9.33 × 10−7 | HMGA1 | 3191 | |
| BFT | WU_10.2_18_56654365 (–––) |
18 | 51,759,775 | ––– | 0.12 | 12.66 | 5.80 × 10−16 | HECW1 | Within |
| WU_10.2_16_23509998 (–––) |
16 | 22,361,911 | ––– | 0.12 | 12.38 | 1.27 × 10−15 | NIPBL | Within | |
| WU_10.2_8_138925750 (–––) |
8 | 129,537,879 | ––– | 0.12 | 11.94 | 4.37 × 10−15 | SNCA | 266,751 | |
| ALGA0014052 (rs81360052) |
2 | 82,412,427 | Intron variant, noncoding transcript variant | 0.14 | 7.72 | 4.52 × 10−10 | TMEM174 | 75,272 | |
| ALGA0040227 (rs80983858) |
7 | 30,176,520 | Downstream gene variant | 0.39 | 5.01 | 6.14 × 10−7 | GRM4 | 2785 | |
| (b) | |||||||||
| Trait | SNP | CHR | POS (bp) | Consequence | MAF | PVE (%) | P-adj | Nearest Gene | DIS (bp) |
| a.LD | WU_10.2_16_23509998 (–––) |
16 | 22,361,911 | ––– | 0.12 | 7.94 | 2.34 × 10−10 | NIPBL | Within |
| WU_10.2_8_138925750 (–––) |
8 | 129,537,879 | ––– | 0.12 | 7.44 | 8.95 × 10−10 | SNCA | 266,751 | |
| WU_10.2_18_56654365 (–––) |
18 | 51,759,775 | ––– | 0.12 | 7.36 | 1.14 × 10−9 | HECW1 | Within | |
| ALGA0014052 (rs81360052) |
2 | 82,412,427 | Intron variant, noncoding transcript variant | 0.14 | 6.95 | 3.38 × 10−9 | TMEM174 | 75,272 | |
| H3GA0000048 (rs80803041) |
1 | 493,510 | Intergenic variant | 0.01 | 4.75 | 1.19 × 10−6 | ERMARD | 19,168 | |