Whole-Genome Resequencing of 299 Large White Pigs Identifies RASAL2 as a Candidate Gene for Feed Efficiency Traits.

Abstract

Feed efficiency is a core economic trait in pig breeding, with feed costs accounting for 60%-70% of total production expenses. Deciphering its genetic basis is critical for precise molecular breeding and the development of grain-saving pig breeds. However, most existing studies rely on SNP arrays, which cannot capture insertion-deletion (InDel) variants, and systematic research on modern intensively selected Large White pig populations remains scarce. In this study, we conducted a genome-wide association study (GWAS) for three core traits-feed conversion ratio (FCR), average daily gain (ADG), and average daily feed intake (ADFI)-using whole-genome resequencing data from 299 purebred Large White pigs, with simultaneous detection of genome-wide single nucleotide polymorphisms (SNPs) and InDels. We identified multiple genomic regions significantly associated with feed efficiency traits. An intronic InDel in RASAL2 represented the strongest FCR association signal. As a specific negative regulator of the Ras signaling pathway, RASAL2 positively regulates preadipocyte differentiation and ameliorates high-fat diet-induced insulin resistance, suggesting it may be associated with feed conversion ratio through energy deposition and metabolic homeostasis. We further annotated 11 additional core candidate genes including TAFA5, TMCC3, BTG1, and PLCB1, which are mainly involved in adipogenesis, energy homeostasis, and skeletal muscle development. These findings enrich genetic resources for porcine feed efficiency research and support molecular marker development for genomic selection in Large White pigs.