Genome-wide association study for rib eye muscle area in a Large White×Minzhu F_2 pig resource population

Rib eye muscle area（REMA） is an economically important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study（GWAS）, the Illumina Porcine SNP60 Bead Chip containing 62 163 single nucleotide polymorphisms（SNPs） was used to genotype 557 pigs from a porcine Large White×Minzhu intercross population. The REMA（at the 5th–6th, 10th–11th and the last ribs） was measured after slaughtered at the age of（240±7） d for each animal. Association tests between REMA trait and SNPs were performed via the Genome-Wide Rapid Association using the Mixed Model and Regression-Genomic Control（GRAMMAR-GC） approach. From the Ensembl porcine database, SNP annotation was implemented using Sus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed significant association with REMA at the last rib at the chromosome-wide significance level. None of the SNPs of REMA at the 5th–6th rib and only a few numbers of the SNPs of REMA at the 10th–11th ribs were found in this study. The Haploview V3.31 program and the Haplo.Stats R package were used to detect and visualize haplotype blocks and to analyze the association of the detected haplotype blocks with REMA at the last rib. A linkage analysis revealed that 4 haplotype blocks contained 4, 4, 2, and 4 SNPs, respectively. Annotations from pig reference genome suggested 2 genes（NOS2, NLK） in block 1（266 kb）, one gene（TMIGD1） in block 2（348 kb）, and one gene（MAP2K4） in block 3（453 kb）. A functional analysis indicated that MYH3 and MYH13 genes are the potential genes controlling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred that NOS2 and NLK genes maybe the main genes of REMA at the last ribs.