Evaluating the effect of ssGBLUP on a composite beef cattle population with limited pedigree completeness

Abstract

To improve the accuracy of estimated breeding values (EBV), correct parentage assignment remains a cornerstone of BLUP. Genomic evaluations can alleviate constraints experienced during the assessment of young animals in large populations, especially for animals with limited pedigree depth and for traits of low heritability. South African (SA) Beefmaster (BMA) breeders mostly are prone to using multiple sires in their herd, with a low parentage verification rate resulting in a larger proportion of young animals with at least one unknown parent. Upgrading of first acceptance cows with blank pedigrees, was common in the establishment of the SA BMA breed. The completeness of a 451,009 animal pedigree, consisting of 187,448 males and 263,561 females dating back to 1937 was assessed. Records for birth weight (BW) and adjusted weights at 205, 365 and 540 days of age (WW, YW, M18W) were collated for the growth multi-trait model, while the fertility multi-trait model included records for adjusted weight at 205 days of age (WW), heifer fertility (HF) and the first three inter-calving periods (ICP). Breeding values and trait reliabilities for registered animals, were either estimated traditionally (BLUP) or with the inclusion of genomic information (ssGBLUP). Genomic profiles of 1,397 recorded animals, genotyped across five commercial single nucleotide polymorphism (SNP) arrays of varying densities, were imputed to a reference genotype of ~132,000 SNPs. Animals with varying proportions of known ancestry allowed for a comparison of genotyped animals across the herd book status of upgrading. The assessment of pedigree completeness indicated a substantial decay in pedigree depth, higher in females compared to males, after the grand-parent generational equivalent. The ssGBLUP accuracies were higher across all traits (0.01 – 0.89), with equal increases observed for animals with limited pedigree depth (only 1 or 2 generations) as to young animals with minimal to no measured phenotypes. The change between conventional and genomic breeding values decreased as the depth of pedigree increased. The results obtained indicate the knowledge of genetic relationships through ssGBLUP allow for increased reliability of predictions for foundation animals with limited or unknown pedigree structure.