Genomic analysis of breed composition and population structure in Montana composite cattle

The Montana composite was developed in Brazil from crosses between Bos indicus and Bos taurus and structured into four biological types: Zebu (N), adapted taurine (A), British taurine (B), and continental taurine (C). This study aimed to characterize the genetic diversity and population structure of the Montana composite using genomic data through principal component analysis (PCA), admixture analysis, and Wright's F_ST statistic. The PCA revealed a clear separation between Bos indicus and Bos taurus groups, with Montana animals distributed in an intermediate position. The first two principal components explained 69.48% and 3.45% of the total variation, respectively. Supervised admixture estimates indicated a predominance of taurine contribution, with type A accounting for 34.47%, 52.64%, and 51.71% at K = 4, 9, and 11, respectively. Increasing the ancestry resolution refined the contribution of individual founder breeds without changing the overall predominance of taurine ancestry. Comparisons between breed proportions obtained from pedigree and genomic data revealed significant differences, for most biological types and ancestry models (P < 0.001), indicating that realized breed composition deviates from theoretical expectations. Estimates of genetic differentiation confirmed greater divergence between Zebu and taurine groups, as well as reduced distances among populations sharing common ancestry. Specific relationships were identified between the composite and some of its founder breeds, particularly Belmont Red, Senepol, and Tuli. Overall, the results demonstrate that the Montana composite has a complex genomic structure, with genomic ancestry varying according to the resolution adopted and differing from pedigree-based expectations.