GWAS on imputed whole-genome sequence variants reveal novel candidate mutations affecting feed efficiency and body composition traits in a crossbred swine population

Abstract A pig’s ability to convert consumed feed into saleable meat is an important component of production efficiency in the swine industry. Given the polygenic and environmentally influenced nature of feed efficiency and body composition traits, conventional selection approaches have limited ability to pinpoint causal genetic factors driving variation. In this study, we performed a single-step genome-wide association study, with whole-genome sequence data (imputed from 50 to 60K SNP arrays), for feed efficiency and body composition traits using a multi-generational crossbred swine population. Overall, the three-generation pedigree consisted of 14,242 pigs, of which 9,336 pigs were phenotyped and 7,339 were genotyped. Whole-genome sequence variants were clustered into 705,923 linkage disequilibrium (LD) blocks, ranging from 0.001 to 9981.80 kb in size. A total of 133 LD blocks were significantly associated with the studied traits, several with potentially large pleiotropic effects. A total of 453 candidate genes were identified in the genomic regions of significant LD blocks. Four functional candidate genes (SIRT2, RYR1, MC4R, and LEPR) were found to harbor moderate to high impact variants, expected to affect protein function.