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

## TL;DR

This study identifies genetic variants and candidate genes linked to intersex and aproctia in Large White pigs, offering insights for improving pig breeding and reducing mortality.

## Contribution

The study reveals novel genetic markers and candidate genes associated with intersex and aproctia in pigs using GWAS and SWIM imputation.

## Key findings

- 53 significant SNPs were identified, with 52 linked to intersex and 1 to aproctia.
- Candidate genes MAD1L1, ID4, EFNA5, and ARNT2 were associated with intersex and aproctia.

## Abstract

We conducted a genome-wide association study (GWAS) on 1030 Large White pigs to investigate the genetic mechanisms underlying congenital developmental abnormalities, specifically intersex and aproctia. We applied mixed linear models (MLMs) to identify genetic variants significantly associated with these traits using both chip data and SWIM-imputed data. A total of 53 significant single-nucleotide polymorphisms (SNPs) were identified, with 52 linked to intersex and 1 to aproctia. Functional annotation revealed fifteen candidate genes for intersex (e.g., MAD1L1, ID4, and EFNA5) and four for aproctia (e.g., ARNT2). These findings enhance our understanding of the genetic mechanisms underlying intersex and aproctia in piglets and provide novel insights for further exploration of the genetic basis of these congenital developmental disorders. The identified markers may serve as potential targets for molecular breeding programs aimed at reducing piglet mortality and improving production efficiency.

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.