Genome-Wide Identification of Quantitative Trait Loci and Candidate Genes for Seven Carcass Traits in a Four-Way Intercross Porcine Population

Abstract BackgroundCarcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs. Results A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 53 SNPs were identified for seven carcass traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The heritability estimates based on SNP for seven carcass traits ranged from 0.23 (loin eye thickness) to 0.48 (dressing percentage). Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found to be associated with carcass traits in pigs. Conclusions A total of 30 significant SNPs, two QTLs on SSC8and SSC10, and 11 candidate genes were identified as being associated with carcasstraits of pigs. The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.