Estimation of genomically enhanced breeding values, and their validation accuracies in the Afrikaner and Brahman beef cattle breeds of South Africa.

Breeding programmes based on the estimated breeding values (EBV) evaluated using performance and pedigree information have slower rates of genetic gain. More so for traits expressed later in an animal’s life and/or are difficult to measure (e.g. fertility, health and fitness). Genomic selection is a well-established technology designed to accelerate genetic gain by enabling more accurate selection of candidates at an earlier stage. Therefore, the objective of this study was to determine the accuracy of predicted genomically enhanced breeding values (GEBV) for growth and reproduction traits. Pedigree data consisted of 226 172 and 862 277 for Afrikaner and Brahman cattle, respectively. Performance data for the Afrikaner consisted of 104 851 and 12 825 records for growth and reproduction traits, respectively, while for Brahman the corresponding data included 256 565 and 91 287 records. Genotyped animals were 456 for Afrikaner and 399 for Brahman, both genotyped for 141 716 SNP markers. Significant effects for inclusion in the final model were determined in R-CRAN using lme4 package. Bivariate analyses were launched using Blupf90 programs, where the Pedigree-based Best Linear Unbiased Prediction (PBLUP) was implemented to estimate pedigree-based breeding values while Single-Step Genomic Best Linear Unbiased Prediction (ssGBlup) was implemented to estimate GEBV. The prediction accuracy was measured as the prediction error variance. Heritability of the traits ranged from low (0.09±0.02) for calving interval (CI) to moderate (0.48±0.01) for average daily gain (ADG) in the Afrikaner cattle. Heritability ranged from low (0.06±0.00) for age at first calving (AFC) to moderate (0.39) for ADG in Brahman. Improvement in prediction accuracy of breeding values, achieved from genomic information ranged from (0.03–0.05) for Afrikaner and from (0.05 - 0.31) for Brahman. The observed results indicated that the addition of genomic information increases the accuracy of EBV for young individuals without their own phenotypes, which may then allow early selection of breeding animals.