Genetic parameters, genomic scans, and gene-set analysis of semen traits in Italian Brown Swiss dairy cattle

The overall goal of this study was to reveal the genetic basis of semen production and quality traits in Italian Brown Swiss dairy cattle. Data consisted of 15,037 ejaculates from a total of 1,591 bulls. Semen traits evaluated were volume, concentration, number of spermatozoa, total motility, and progressive motility. A subset of 1,102 bulls also had records for sire conception rate, as a measure of reproductive success. We estimated the heritability and repeatability of semen traits and their genetic correlations with sire conception rate using univariate and bivariate animal models. We also identified candidate genes for semen traits using single-step genomic scans with 438k SNP markers and revealed gene networks and biological pathways through functional gene-set analyses. Heritabilities ranged from 0.04 for progressive motility to 0.23 for volume, indicating the possibility of improving these traits through selective breeding. Repeatabilities were considerably higher than the heritabilities, especially for sperm motility, indicating that both nonadditive effects and the permanent environment significantly affect bull fertility. We found low to moderate genetic correlations among sperm traits, and of particular interest, high genetic correlations between sperm motility and sire conception rate, indicating the predictive values of these traits for sire reproductive success. Genomic scans revealed regions on BTA4 and BTA11 highly associated with total and progressive motility. These regions harbor genes, such as RPS27A, CCDC88A, CFAP36, SPMIP4, and DNAAF1, that are all directly implicated in sperm motility. The gene-set analyses revealed functional terms related to sperm biology, male fertility, fertilization, and the immune system, among others. Overall, our study contributes to a better understanding of the genetic basis of dairy bull fertility. In addition, our findings may guide the development and deployment of novel strategies for improving service sire fertility in Brown Swiss cattle.