Genome-wide association study of three litter traits in Yorkshire pigs

Abstract

Litter traits are important in the development of production and economic profits of pigs. The object of this study was to perform genome-wide association studies (GWASs) for the total number born (TNB), number born alive (NBA) and number born healthy (NBH) traits in a Yorkshire population. By mixed model, we conducted GWASs with gcta software, and in total identified 3, 7 and 12 significant SNPs associated with TNB, NBA and NBH respectively: one on Sus scrofa chromosome (SSC) 2 (p = 7.03 × 10^-5 ), one on SSC4 (p = 8.53 × 10^-5 ), two on SSC 6 (p = 9.27 × 10^-5 to 9.64 × 10^-5 ), nine on SSC 8 (p = 1.53 × 10^-5 to 8.52 × 10^-5 ), four on SSC 14 (p = 2.17 × 10^-5 to 6.79 × 10^-5 ), and one on SSC 15 (p = 9.30 × 10^-5 ). We screened for flanking regions ±1 Mb nearby or within the significant SNPs, and found 203 candidate genes, including 53 for TNB, 71 for NBA and 112 for NBH. In conclusion, our findings show the significant SNPs with candidate genes for the TNB, NBA and NBH traits in Yorkshire pigs.

Keywords: Yorkshire pigs; genome-wide association studies; number born alive; number born healthy; total number born.