Genetic Architecture of Semen Production Traits in Duroc Boars Accounting for X‐Chromosome and Non‐Additive Genetic Effects

Semen production traits are key indicators of reproductive performance in pigs. Their genetic architecture, particularly the contribution of the X-chromosome and non-additive genetic effects, remains poorly understood. We investigated contributions of the X-chromosome and non-additive genetic effects to semen production traits in Duroc boars using genetic parameter estimation and genome-wide association studies (GWAS). Overall, 13,788 records from 502 Duroc boars genotyped with high-density single-nucleotide polymorphism (SNP) arrays were analyzed for semen volume (VOL), sperm number (NUM), sperm concentration (CON), and the proportion of morphologically abnormal sperm (PAS). Genetic parameters were estimated using pedigree- and SNP-based repeatability animal models. A GWAS was performed using 40,197 SNPs on the autosomal chromosomes and 1521 on the X chromosome. The results of pedigree-based analyses indicated that permanent environmental effects substantially contributed to repeatability. The SNP-based analyses revealed that epistatic effects accounted for a large proportion of the variance in NUM and PAS, whereas their contributions were limited for VOL and CON. The X-chromosome effects explained little phenotypic variance across all traits. No significant loci were detected in the GWAS using additive models; no substantial X-linked associations were identified. A significantly associated SNP with NUM on chromosome 1 (rs80957931) was identified in the non-additive model.