Breed Composition and Heterozygosity in Brangus and Braford Composite Cattle Breeds

Composite cattle breeds are developed to combine favorable traits from parental populations and to exploit heterosis across diverse production environments. However, their genomic structure becomes progressively more complex across generations, and it remains unclear to what extent patterns of local ancestry and heterozygosity are conserved across breeds. The objective of this study was to characterize genomic breed composition in Argentine Brangus and Braford at both global and local levels, and to identify shared genomic segments with extreme values of indicine ancestry and heterozygosity. A total of 783 animals from six breeds were analyzed using SNP data. Global ancestry proportions were estimated using STRUCTURE, whereas local ancestry was inferred through haplotype phasing (Shapeit5) and local ancestry inference using LOTER. Deviations between observed and expected breed composition and heterozygosity were evaluated at the SNP level using chi-square tests with multiple testing correction. Shared genomic segments were defined as contiguous genomic intervals composed of SNPs showing significant deviations in both breeds. Brangus and Braford showed lower indicine proportions than the expected 37.5%, with reductions of 1.2% and 7.1%, respectively. Local ancestry analysis revealed heterogeneous genomic patterns, with shared segments enriched for indicine ancestry on chromosomes 3, 6, 20, and 28. In contrast, segments with reduced indicine ancestry were more broadly distributed. No SNP exceeded the expected heterozygosity; however, multiple regions showed significant reductions, particularly on chromosome 18. These results demonstrate that Brangus and Braford exhibit complex and heterogeneous genomic architectures, with shared genomic regions showing extreme patterns of ancestry and heterozygosity.