A look under the hood of genomic-estimated breed compositions for brangus cattle: What have we learned?

Abstract

The Brangus cattle were developed to utilize the superior traits of Angus and Brahman cattle. Their genetic compositions are expected to be stabilized at 3/8 Brahman and 5/8 Angus. Previous studies have shown more than expected Angus lineage with Brangus cattle, and the reasons are yet to be investigated. In this study, we revisited the breed compositions for 3,605 Brangus cattle from three perspectives: genome-wise (GBC), per chromosomes (CBC), and per chromosome segments (SBC). The former (GBC) depicted an overall picture of the “mosaic” genome of the Brangus attributable to their ancestors, whereas the latter two criteria (CBC and SBC) corresponded to local ancestral contributions. The average GBC for the 3,605 Brangus cattle were 70.2% Angus and 29.8% Brahman. The K-means clustering supported the postulation of the mixture of 1/2 Ultrablack (UB) animals in Brangus. For the non-UB Brangus animals, the average GBC were estimated to be 67.4% Angus and 32.6% Brahman. The 95% confidence intervals of their overall GBC were 60.4%–73.5% Angus and 26.5%–39.6% Brahman. Possibly, genetic selection and drifting have resulted in an approximately 5% average deviation toward Angus lineage. The estimated ancestral contributions by chromosomes were heavily distributed toward Angus, with 27 chromosomes having an average Angus CBC greater than 62.5% but only two chromosomes (5 and 20) having Brahman CBC greater than 37.5%. The chromosomal regions with high Angus breed proportions were prevalent, tending to form larger blocks on most chromosomes. In contrast, chromosome segments with high Brahman breed proportion were relatively few and isolated, presenting only on seven chromosomes. Hence, genomic hitchhiking effects were strong where Angus favorable alleles resided but weak where Brahman favorable alleles were present. The functions of genes identified in the chromosomal regions with high (≥75%) Angus compositions were diverse yet may were related to growth and body development. In contrast, the genes identified in the regions with high (≥37.5%) Brahman compositions were primarily responsible for disease resistance. In conclusion, we have addressed the questions concerning the Brangus genetic make-ups. The results can help form a dynamic picture of the Brangus breed formation and the genomic reshaping.

MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver

“…Although Angus and Brahman cattle differ by ∼1% genetically at the nucleotide level and have a different Y chromosome structure ( Goldammer et al, 1997 ; Low et al, 2020 ), they produce fertile inter-subspecific hybrids ( Hiendleder et al, 2008 ) that have enabled the investigation of genetic and epigenetic factors involved in phenotypic differences of quantitative traits ( Hiendleder et al, 2008 ; Mao et al, 2008 ; Xiang et al, 2013 ; Xiang et al, 2014 ; Akanno et al, 2018 ; Gobena et al, 2018 ; Andrade et al, 2022 ). Genetic and epigenetic regulatory changes that underlie the phenotypic differences between taurine and indicine cattle are of substantial interest from both scientific and economic perspectives, i.e., understanding complex trait biology and using this knowledge to combine desirable traits from both subspecies ( Li et al, 2023 ).…”