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Genomic prediction of dairy bull fertility using X chromosome markers.

H. A. Pacheco




Genomic prediction of dairy bull fertility using X chromosome markers.
H. A. Pacheco*1, F. M. Rezende1,2, F. Pe�agaricano1. 1University of Florida Gainesville, FL, 2Universidade Federal de Uberl�ndia Uberl�ndia, MG, Brazil.

Service sire has been recognized as an important factor affecting dairy herd fertility. Our group has reported promising results on 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, our goal was to evaluate the genomic prediction of service sire fertility including SNP markers on the X chromosome (BTAX). Data set consisted of 5,014 Holstein bulls with sire conception rate records and genotypes for roughly 291k SNP located on the autosomes, 1.5k SNP located on the pseudoautosomal region (PAR), and 13.7k X-specific SNP. The analyses included linear and Gaussian kernel-based models fitting either only SNP markers on autosomes (291k SNPs) or combining autosomal with PAR and X-specific SNP markers (291k SNPs + 15.2k SNPs). Predictive performance was evaluated using 10-fold cross-validation repeated 10 times. Interestingly, the linear kernel model that included the BTAX markers exhibited a higher average predictive correlation than the linear kernel model that fitted only autosomal SNPs (0.338 vs 0.319). The prediction of bull fertility was further improved by using a Gaussian kernel-based model combining autosomal and BTAX SNPs. Indeed, this model fitting markers on 'autosomes + BTAX' delivered an average predictive correlation equal to 0.343, representing an increase in predictive ability of about 7.5% compared with the standard whole autosomal genome model. Overall, our findings indicate that including markers on the X chromosome would benefit the genomic prediction of bull fertility. These results may help to improve conception rates in dairy herds through accurate genome-guided decisions on bull fertility.

Keywords: kernel-based prediction models, sex chromosomes, sire conception rate.