Table 2 Significant SNPs and candidate genes for average daily gain and lean meat percentage in the single-population GWAS
Trait1 (population) | SNP2 | SSC3 | Location4 (bp) | EPV5 (%) | P-value6 | Distance7 (bp) | Candidate gene |
|---|---|---|---|---|---|---|---|
ADG (AD) | H3GA0003149 | 1 | 162,192,627 | 0.91 | 6.07 × 10− 7 | within | ALPK2 |
WU_10.2_1_179575045 | 1 | 161,987,727 | 0.92 | 7.45 × 10− 7 | within | ENSSSCG00000004911 | |
ALGA0006684 | 1 | 161,853,405 | 0.93 | 4.49 × 10− 6 | within | ENSSSCG00000004911 | |
MARC0013872 | 1 | 161,824,864 | 0.79 | 1.12 × 10− 5 | within | ENSSSCG00000004911 | |
ASGA0004988 | 1 | 159,881,634 | 0.83 | 1.15 × 10− 5 | within | CDH20 | |
ALGA0006623 | 1 | 160,347,188 | 0.76 | 2.31 × 10− 5 | within | ENSSSCG00000048538 | |
Affx-114,594,216 | 6 | 168,268,278 | 0.65 | 3.28 × 10−7 | 13,851 | ENSSSCG00000039458 | |
DIAS0000782 | 8 | 30,256,709 | 0.45 | 2.51 × 10−5 | 32,698 | TMEM156 | |
WU_10.2_11_86301815 | 11 | 78,432,491 | 0.66 | 2.09 × 10− 5 | within | MCF2L | |
WU_10.2_14_8843751 | 14 | 7,988,327 | 0.24 | 1.97 × 10−5 | −26,761 | STC1 | |
LMP (AD) | WU_10.2_1_179575045 | 1 | 161,987,727 | 0.47 | 3.22 × 10− 6 | within | ENSSSCG00000004911 |
H3GA0003149 | 1 | 162,192,627 | 0.47 | 3.24 × 10− 6 | within | ALPK2 | |
MARC0013872 | 1 | 161,824,864 | 0.65 | 6.00 × 10− 6 | within | ENSSSCG00000004911 | |
ALGA0006684 | 1 | 161,853,405 | 0.60 | 1.25 × 10−5 | within | ENSSSCG00000004911 | |
ALGA0006623 | 1 | 160,347,188 | 0.59 | 1.38 × 10−5 | within | ENSSSCG00000048538 | |
ALGA0123800 | 1 | 254,207,127 | 1.48 | 1.99 × 10−5 | within | RGS3 | |
ASGA0004988 | 1 | 159,881,634 | 0.51 | 2.13 × 10−5 | within | CDH20 | |
WU_10.2_2_82907810 | 2 | 81,306,158 | 1.44 | 5.91 × 10−6 | − 3295 | SNCB | |
10,006,986 | 2 | 76,416,246 | 1.10 | 7.03 × 10− 6 | within | AMH | |
ASGA0096606 | 6 | 48,241,180 | 1.01 | 5.17 × 10−10 | −31,313 | LGALS13 | |
ASGA0091829 | 6 | 48,289,460 | 0.71 | 2.07 × 10−7 | 16,384 | DYRK1B | |
WU_10.2_6_41924003 | 6 | 46,461,817 | 0.87 | 7.05 × 10−6 | within | ZNF570 | |
Affx-114,594,216 | 6 | 168,268,278 | 0.41 | 1.87 × 10−5 | 13,851 | ENSSSCG00000039458 | |
ALGA0105911 | 12 | 27,109,190 | 1.23 | 6.92 × 10−6 | − 8767 | WFIKKN2 | |
WU_10.2_15_156432561 | 15 | 57,333,035 | 0.58 | 3.08 × 10−6 | within | ARHGEF4 | |
ADG (CD) | ASGA0004970 | 1 | 158,589,475 | 0.94 | 1.66 × 10−5 | 53,338 | PHLPP1 |
LMP (CD) | ASGA0002401 | 1 | 38,161,769 | 2.75 | 1.87 × 10−6 | within | NKAIN2 |
MARC0034815 | 1 | 38,185,044 | 2.75 | 1.87 × 10−6 | within | NKAIN2 | |
MARC0026342 | 1 | 38,189,919 | 2.75 | 1.87 × 10−6 | within | NKAIN2 | |
H3GA0001475 | 1 | 37,366,714 | 2.18 | 2.78 × 10−6 | − 135,329 | HEY2 | |
DRGA0000591 | 1 | 37,381,311 | 2.12 | 4.48 × 10−6 | −149,926 | HEY2 | |
MARC0114211 | 1 | 37,401,594 | 2.12 | 4.48 × 10−6 | − 170,209 | HEY2 | |
DRGA0000604 | 1 | 38,067,414 | 2.09 | 6.49 × 10−6 | within | NKAIN2 | |
ASGA0101182 | 1 | 37,746,276 | 2.06 | 8.68 × 10−6 | within | TPD52L1 | |
MARC0013872 | 1 | 161,824,864 | 1.76 | 1.02 × 10−5 | within | ENSSSCG00000004911 | |
ASGA0004988 | 1 | 159,881,634 | 1.74 | 1.33 × 10− 5 | within | CDH20 | |
ALGA0006602 | 1 | 159,538,854 | 1.72 | 1.53 × 10−5 | within | RNF152 | |
H3GA0003104 | 1 | 159,619,891 | 1.72 | 1.53 × 10−5 | −17,910 | RNF152 | |
H3GA0001466 | 1 | 37,024,102 | 1.18 | 1.76 × 10−5 | −172 | HINT3 | |
ALGA0006623 | 1 | 160,347,188 | 1.72 | 1.77 × 10−5 | within | ENSSSCG00000048538 | |
WU_10.2_1_178188861 | 1 | 160,447,734 | 1.72 | 1.77 × 10−5 | 98,849 | ENSSSCG00000048538 | |
INRA0004898 | 1 | 158,811,662 | 1.64 | 2.46 × 10−5 | within | PHLPP1 | |
MARC0075909 | 1 | 159,238,083 | 1.66 | 2.51 × 10−5 | within | RELCH | |
ASGA0020293 | 4 | 74,693,408 | 1.38 | 9.37 × 10−6 | within | FAM110B | |
H3GA0013036 | 4 | 74,714,319 | 1.38 | 9.37 × 10− 6 | within | FAM110B | |
MARC0093868 | 4 | 74,774,997 | 1.38 | 9.66 × 10−6 | −29,012 | FAM110B |