Genome-Wide Association Study Reveals Genetic Mechanisms Underlying Intersex and Aproctia in Large White Pigs

Congenital developmental abnormalities in piglets, such as intersex and aproctia, adversely affect survival rates, growth performance, and genetic breeding efficiency in pig populations. To elucidate their genetic basis, we performed a genome-wide association study (GWAS) on 1030 Large White pigs. We combined 50 K SNP chip data with SWIM-based genotype imputation to enhance the resolution of genetic variation detection, followed by MLM analysis. Our results identified 53 significant SNPs, with 52 associated with intersex and 1 with aproctia. Key candidate genes included MAD1L1, ID4, EFNA5, and PPP1R16B for intersex and ARNT2 for aproctia. Functional enrichment analysis highlighted pathways related to gonadal development (e.g., progesterone-mediated oocyte maturation) and embryonic morphogenesis. Collectively, the identification of these SNPs and candidate genes advances our understanding of the genetic architecture of intersex and aproctia in piglets. These findings provide actionable insights for optimizing genetic breeding strategies and improving health management in Large White pig production, with potential implications for reducing economic losses caused by congenital disorders.