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Table 2 Location of and gene information for SNPs associated (P < 1 × 10 -4 ) with meat quality traits

From: The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study

Trait Chromosome SNPs Position Alleles MAF1 P_value2 P_adjust3 R2 4 Nearest Gene Distance (Kb)5
DMBr 2 Gga_rs14206277 78152161 G/A 0.338 2.01E-05 0.34 0.071 FAM105A within
DMTh 14 Gga_rs14086206 14720651 A/G 0.340 8.38E-05 1.40 0.077 TBC1D24 D 20.6
DMBr Z GGaluGA346234 1626487 G/A 0.016 1.16E-05 0.19 0.075 ST8SIA5 within
IMFBr 1 Gga_rs13878108 65617257 G/A 0.240 6.49E-05 1.09 0.063 MGST1 D 183.1
IMFBr 3 GGaluGA217414 40654853 A/G 0.116 9.30E-05/2.59E-06 1.56 0.061 NTPCR U 109.9
IMFBr 4 GGaluGA255658 43311293 G/A 0.100 3.46E-05/5.61E-09 0.58 0.057 AGA U 330.8
IMFBr 5 Gga_rs14524377 27009717 G/A 0.193 5.41E-05 0.91 0.066 TYRO3 U 73.6
IMFBr Z GGaluGA348872 18701354 A/G 0.025 2.14E-05/4.28E-07 0.36 0.059 KIF2A U 122.3
Meat color          
L* 2 GGaluGA137635 23472767 A/G 0.302 7.04E-05 1.18 0.068 COL1A2 U 58.0
L* 18 GGaluGA121429 6990031 C/A 0.412 8.96E-05 1.50 0.065 KPNA2 U 0.2
L* 18 GGaluGA121456 7112093 G/A 0.383 7.19E-05 1.21 0.068 PSMD12 U 34.3
b* 27 Gga_rs15237721 1597620 G/A 0.364 4.85E-05 0.81 0.077 FTSJ3 U 2.4
Skin color           
L* 2 GGaluGA159190 99182734 G/A 0.122 7.62E-05 1.28 0.073 PTPN2 U 130.6
L* 13 Gga_rs14058862 10586210 A/G 0.114 9.39E-05 1.57 0.071 SPINK5 U 28.1
L* 13 Gga_rs15697794 11284741 G/A 0.049 9.61E-05 1.61 0.058 CLINT1 U 15.6
L* 21 Gga_rs16180462 3645146 G/A 0.162 8.76E-05 1.47 0.072 PGD U 62.7
a* 19 Gga_rs15044922 2083895 G/A 0.213 5.10E-05 0.85 0.077 MIR1587 D 301.0
b* 6 GGaluGA305921 33306370 A/G 0.412 3.24E-05 0.54 0.089 BUB3 D 195.5
  1. 1MAF minor allele frequency; 2the bold p-values of SNPs are the genome-wide significance by the general linear model (GLM); 3p-adjust indicates the p-value adjusted by “LD adjusted” Bonferroni; 4R2, SNP indicates the ratio of phenotypic variation; 5U indicates that the SNP is upstream of the gene, while D indicates that the SNP is downstream of the gene. These abbreviations are also used in Table 3.