Genome-Wide Association Study Identifies Candidate Genes of Boar Semen Quality Traits

Semen quality is the most crucial indicator for evaluating the reproductive capacity of boars. Semen traits, including semen volume, sperm density, motility and abnormality rate, exhibit low to moderate heritability, making genetic improvement through conventional breeding challenging. Advances in genome sequencing have enabled GWAS to identify genetic markers for economically important traits. In this study, 172 Large White boars with 56,427 phenotypic records across seven semen quality traits were subjected to 15× whole-genome resequencing. GWAS was performed using the FarmCPU model, identifying 2824 significant SNPs and annotating 573 candidate genes associated with seven semen traits. After linkage disequilibrium (LD)-based clumping (r² < 0.1, 1 Mb window), 916 independent genomic loci were identified as significantly associated with the seven semen quality traits. Functional analysis revealed key biological processes, including growth regulation, extrinsic apoptotic signalling pathway and the TOR signalling pathway. In an expanded population, six SNPs associated with semen quality traits were identified in the SOX6, CACNA1H, FOXP4, EFNA3 and ITGA9 genes. Significant associations were found between SOX6 gene and sperm abnormality rate, CACNA1H gene and semen volume, sperm density, motility, and abnormality rate, FOXP4 gene and sperm density, EFNA3 gene and semen volume, sperm density, ITGA9 gene and semen volume, sperm density, motility, and abnormality rate. These findings enhance understanding of the genetic architecture of boar semen quality and provide molecular markers for genetic selection, facilitating improved breeding strategies.