Genomic selection for female reproduction in Australian tropically adapted beef cattle

Abstract

The usefulness of genomic selection was assessed for female reproduction in tropically adapted breeds in northern Australia. Records from experimental populations of Brahman (996) and Tropical Composite (1097) cattle that had had six calving opportunities were used to derive genomic predictions for several measures of female fertility. These measures included age at first corpus luteum (AGECL), at first calving and subsequent postpartum anoestrous interval and measures of early and lifetime numbers of calves born or weaned. In a second population, data on pregnancy and following status (anoestrous or pregnancy) were collected from 27 commercial herds from northern Australia to validate genomic predictions. Cows were genotyped with a variety of single nucleotide polymorphism (SNP) panels and, where necessary, genotypes imputed to the highest density (729 068 SNPs). Genetic parameters of subsets of the complete data were estimated. These subsets were used to validate genomic predictions using genomic best linear unbiased prediction using both univariate cross-validation and bivariate analyses. Estimated heritability ranged from 0.56 for AGECL to 0.03 for lifetime average calving rate in the experimental cows, and from 0.09 to 0.25 for early life reproduction traits in the commercial cows. Accuracies of predictions were generally low, reflecting the limited number of data in the experimental populations. For AGECL and postpartum anoestrous interval, the highest accuracy was 0.35 for experimental Brahman cows using five-fold univariate cross-validation. Greater genetic complexity in the Tropical Composite cows resulted in the corresponding accuracy of 0.23 for AGECL. Similar level of accuracies (from univariate and bivariate analyses) were found for some of the early measures of female reproduction in commercial cows, indicating that there is potential for genomic selection but it is limited by the number of animals with phenotypes.