Whole-genome sequence-based association analyses on an eight-breed crossed heterogeneous stock of pigs reveal the genetic basis of skeletal muscle fiber characteristics

Skeletal muscle fiber characteristics (MFCs) have been extensively studied due to their importance to human health and athletic ability, as well as to the quantity and quality of livestock meat production. Hence, we performed a genome-wide association study (GWAS) on nine muscle fiber traits by using whole genome sequence data in an eight-breed crossed heterogeneous stock pig population. This GWAS revealed 67 quantitative trait loci (QTLs) for these traits. The most significant GWAS signal was detected in the region of Sus scrofa chromosome 12 (SSC12) containing the MYH gene family. Notably, we identified a significant SNP rs322008693 (P = 7.52E-09) as the most likely causal mutation for the total number of muscle fibers (TNMF) QTL on SSC1. The results of EMSA and luciferase assays indicated that the rs322008693 SNP resided in a functional element. These findings provide valuable molecular markers for pig meat production selection as well as for deciphering the genetic mechanisms of the muscle fiber physiology.