Genome-Wide Association and Meta-Analysis Identify Candidate Genes for Sperm Freezability in Duroc and Yorkshire Boars

Boar sperm freezability (SF) is an economically important trait that influences reproductive efficiency and genetic improvement in pigs. However, its genetic basis remains poorly understood. In this study, semen samples from 382 Duroc and 151 Yorkshire boars were evaluated for sperm motility and recovery rate, and all individuals were genotyped using an 80K SNP array. Within-breed GWAS were first conducted, followed by a meta-analysis integrating the GWAS results from both boars. Individuals were classified into GSF and PSF groups based on sperm recovery rate for subsequent selection signature analysis. The results showed that Duroc boars exhibited significantly higher SF than Yorkshire boars. Heritability estimates for SF were moderate, with values of 0.35 in Duroc and 0.30 in Yorkshire. GWAS identified 10 significant SNPs in Duroc and 33 in Yorkshire associated with SF. Meta-analysis further detected 12 significant SNPs, annotated to candidate genes such as CCDC181, PARN, SOX9, and NCKAP5L. Association analysis identified ten representative variants significantly correlated with sperm recovery rate, with variants in PARN and MAP2K6 showing strong additive effects. Selection signature analysis revealed multiple genomic regions under differential selection between GSF and PSF groups, identifying several candidate genes associated with SF. Functional enrichment analysis indicated that these genes are mainly involved in spermatogenesis, flagellar motility, cellular stress response, and cold adaptation pathways. Overall, this study provides novel insights into the genetic architecture of boar SF and identifies potential molecular markers for genetic improvement and functional genomic studies in pigs.