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.