Gene mapping and genomic prediction of bull fertility using sex chromosome markers

Service sire has been recognized as an important factor affecting dairy herd fertility. Our group has reported promising results on gene mapping and genomic prediction of dairy bull fertility using autosomal SNP markers. Little is known, however, about the genetic contribution of sex chromosomes, which are enriched in genes related to sexual development and reproduction. As such, the main goal of this study was to investigate the effect of SNP markers on X and Y chromosomes (BTAX and BTAY, respectively) on sire conception rate (SCR) in US Holstein bulls. The analysis included a total of 5,014 bulls with SCR records and genotypes for roughly 291k SNP located on the autosomes, 1.5k SNP located on the pseudoautosomal region (PAR), 13.7k BTAX-specific SNP, and 24 BTAY-specific SNP. We first performed genomic scans of the sex chromosomes, and then we evaluated the genomic prediction of SCR including BTAX SNP markers in the predictive models. Two markers located on PAR and 3 markers located on the X-specific region showed significant associations with sire fertility. Interestingly, these regions harbor genes, such as FAM9B, TBL1X, and PIH1D3, that are directly implicated in testosterone concentration, spermatogenesis, and sperm motility. On the other hand, BTAY showed very low genetic variability, and none of the segregating markers were associated with SCR. Notably, model predictive ability was largely improved by including BTAX markers. Indeed, the combination of autosomal with BTAX SNP delivered predictive correlations around 0.343, representing an increase in accuracy of about 7.5% compared with the standard whole autosomal genome approach. Overall, this study provides evidence of the importance of both PAR and X-specific regions in male fertility in dairy cattle. These findings may help to improve conception rates in dairy herds through accurate genome-guided decisions on bull fertility.