An assessment of population genetic structure in Australian beef cattle breeds

Australia's diverse climates and markets have resulted in the use of numerous beef cattle breeds. Genetic evaluations are currently within-breed, with some breeds also implementing single-step genomics. Incorporating pedigree, phenotype and genomic data into multi-breed single-step genetic evaluations remains a challenge. Developing these multi-breed evaluations requires further research, particularly understanding the genomic population structures across breeds. A comprehensive knowledge of these genetic relationships is crucial for developing multi-breed evaluations. The genomic population structure of twelve Australian beef breeds was assessed using 8K SNPs in common across breeds. To avoid bias due to unequal sample sizes, we standardised the number of individuals to 260 per breed. This was achieved by grouping each breed into several genetic clusters based on principal component analysis (PCA) complemented by Gaussian mixture models (GMM) clustering to capture the total genetic diversity within each breed. Then, several population structure analyses (PCA, phylogenetic relationships, and ADMIXTURE) were undertaken to explore the genomic population structure and breed composition. Genomic population structure results demonstrated wide diversity across some breeds and, in particular, highlighted distinct genetic differences between Bos indicus and Bos taurus breeds. Admixed breeds exhibited significant variation, revealing how contributions from multiple ancestral breeds shape the breed's genomic makeup. These findings highlight the value of understanding the genomic population structure for multi-breed genetic evaluations, particularly for admixed breeds, where they may benefit from genomic links to multiple breeds.