Short communication: genomic kinship, opposing homozygotes and genetic diversity in a selected population of Australian Angus cattle

Using molecular genotypes to check for Mendelian inconsistencies allows the identification of animals for which pedigree and genotype information disagree. A further use of molecular data is to understand and manage genetic diversity in a population. We sourced from the Angus Australia database a selected population of 11,224 animals, including 10,309 progeny born between 2013 and 2023 from 269 sires and 646 dams with at least 100 and 10 progeny, respectively. All animals had imputed genotypes for 61,105 autosomal markers. The additive and dominance genomic relationship (GR), as well as the number of opposing homozygotes (OH) were examined for pedigree-based relationship pairs including parent-offspring (PO; 21,307 pairs), full-sibs (FS; 35,486), half-sibs (HS; 677,421), grandparent-grandoffspring (16,308) and unrelated (62,232,954 pairs). Theoretical expectations for means and variances were compared against empirical observations. Consistent with expectations, the variance of additive GR among FS pairs was higher than the variance among HS, and the number of OH among FS was half the number of OH among HS. Expected to be 0.5, the observed additive GR among FS pairs and PO pairs was 0.483 (SD = 0.054) and 0.488 (SD = 0.037), respectively. The correlation (± SE) between additive and dominance GR was near unity for self-relationships (r = 0.935 ± 0.003) and zero for unrelated pairs (r = -0.001 ± 0.000). Expected to be zero, the number of OH among PO pairs averaged 11.6 and 77.5% of all PO pairs had an OH ≤ 12. Among FS pairs, the observed OH averaged 1,162.45 (expected = 1,150.17), and this average was surpassed by only 14 PO pairs, which was attributed to pedigree errors. Crucially, the anticipated negative correlation between additive GR and OH was affected by the degree of kindship being strongest negative among unrelated pairs (r = -0.762 ± 0.001). A principal components analysis and a network-based pipeline revealed the genetic diversity of the population with a focus on the role of the most influential parents. We conclude that, in our selected population of Australian Angus cattle, observed GRs were close to expectations, while Mendelian inconsistencies were very rare and likely attributed to either errors in pedigree recording, mislabeling of samples, or error in genotypes and genotype imputation. Finally, our study reveals the genetic diversity and breeding management decisions occurring in modern Australian Angus breeding programs.