Genetic parameters and genome-wide association analysis of service sire effects on litter size and its relationship with boar semen quality in three terminal sire lines

Abstract Background Reproductive performance is key to efficient and profitable pig production. In selecting boars to enhance overall male reproductive success, the paternal genetic influence on litter size is of particular interest, in addition to semen quality improvement in terminal sire lines. Few studies have investigated the impact of service sire effects on litter size in swine. Previous models often treated the service sire as a non-genetic effect or as a genetic effect but ignoring the additive relationship between service sires and sows. Moreover, no studies have incorporated genomic information when examining service sire genetic effects for litter size in pigs. In this study, we aimed to estimate genetic parameters for service sire additive genetic effects on number born alive (NBA) and conducted a genome-wide association study (GWAS) using large genotyped data sets in pigs. Both service sire and sow effects were modeled as additive genetic effects, considering a covariance structure among them, given by the relationship matrix. The relationship between service sire additive genetic effects on NBA and direct additive genetic effects for boar semen quality traits was also evaluated. Results Estimates of heritability ranged from 0.01 to 0.03 for service sire effects and from 0.09 to 0.15 for sow effects, with their genetic correlation estimates ranging from − 0.20 to 0.37. Results from GWAS showed no strong signals for service sire effects on NBA. Heritability estimates ranged from 0.10 to 0.12 for sperm motility and from 0.17 to 0.28 for total abnormal morphology. Correlations between service sire genomic estimated breeding values for NBA and semen quality were low but in the favorable direction. Conclusions Selection for semen motility might be favorable for improving semen morphology. Although the service sire genetic contribution to litter size was small, the low but favorable correlations between genomic estimated breeding values for litter size and semen quality suggest that incorporating service sire effects together with semen quality traits into selection can improve boar reproductive performance.