Effect of the X chromosome in genomic evaluations of reproductive traits in beef cattle

•Higher heritability estimates were obtained for all the reproductive traits when the X chromosome was included.•Inclusion of the X chromosome in the analysis can improve the prediction of genomic breeding values, especially for SC trait.•A higher loss of prediction ability was obtained for SC when the analysis did not considered the X chromosome.•Analyses that include the X chromosome and all animals provide more reliable genomic breeding value estimates.•The evaluation of reproductive traits should combine X chromosome and autosomal markers. The aim of this study was to evaluate whether there are predictive advantages for breeding values with inclusion of X chromosome genomic markers for reproductive (occurrence of early pregnancy – P16 and age at first calving - AFC) and andrological (scrotal circumference -SC) variables in beef cattle. There were 3263 genotypes of females and males evaluated. There were breeding value estimates for SC, AFC and P16 considering two scenarios: 1) only autosomal markers or 2) autosomal and X chromosome markers. To evaluate effects of inclusion of X chromosome markers on selection, responses to selection were compared including or not including genomic marker information from the X chromosome. There were greater heritability estimates for SC (0.40 and 0.31), AFC (0.11 and 0.09) and P16 (0.43 and 0.38) when analyses included, compared with not including, genomic marker information from the X chromosome. When selection is based on results from analyses that did not include information for the X chromosome, there was about a 7 % lesser mean genomic breeding value for the SC traits for selected animals. For P16, there was an approximate 4% lesser breeding value without inclusion of genomic marker information from the X chromosome, while this inclusion did not have as great an effect on the breeding value for AFC. There was an average predictive correlation of 0.79, 0.98 and 0.84 for SC, AFC and P16, respectively. These estimates indicate inclusion of the X chromosome genomic marker information in the analysis can improve prediction of genomic breeding values, especially for SC.