PSXIV-21 - Genetic diversity in Mashona, a Sanga-type cattle from southern Africa

Abstract: Climate change projections suggest pervasive impacts on livestock performance, for which United States (US) producers will need to adjust. Fortuitously, the US has a broad array of genetic resources among its breeds with which to explore a genetic basis for increased resilience. Sanga-type cattle were developed in a tropical environment and are generally considered a long-formed taurine and indicine composite. Consequently, they may harbor unique genetic diversity which could be of utility to the US cattle industry. Mashona is a Sanga breed from southern Africa and has been imported into the US. Comparison of its genetic diversity to other breeds found in US tropical and subtropical environments has not been studied. To initiate evaluation of Mashona we evaluated 334 animals from Mashona (24), Tuli (12), Florida Cracker (20), Senepol (24), Brahman (68), Brangus (20), Romosinuano (20), Hereford (50), Angus (50) and Wagyu (56). Notably, Tuli is also a Sanga-type breed closely related to Mashona. All animals were genotyped with the BovineHD chip (777K SNP). Quality control included removal of loci with a minor allele frequency < 0.05 and a missingness rate > 0.1. For SNP pairs with r² > 0.2 across all breeds, one SNP was chosen at random and removed. After quality control, 75,698 SNP remained for analysis. The first 4 principal components explained 15.5, 4.3, 3.1, and 2.4%, respectively, of the variation in the genomic relationship matrix. Mashona and Tuli tended to cluster close together for all the principal components (PC) evaluated. The first PC captured variation across the taurine-indicine axis with Hereford and Brahman at opposite extremes; Mashona clustered approximately midway between taurine and indicine breeds. Breed placement along PC4 highlighted separation of Sanga breeds from other breeds evaluated, though Mashona and Tuli each formed a distinct cluster. Ancestral groups were estimated using ADMIXTURE software for k=3 to 15. Cross-validation error declined from 0.55 at k=3 to 0.50 at k=7, after which the error was relatively similar for higher values of k. As early as k=4, Mashona and Tuli were found to be a distinct population. This group represented 61.7-99.9 and 59.5-74.9% of the estimated admixture for Mashona and Tuli, respectively. At k=10, Mashona and Tuli branched into separate populations. Additional estimated ancestry in Mashona was primarily from groups representing Angus and Brahman, up to 15 and 9%, respectively. With progressive cluster number tropical cattle breeds were found to be distinct from one another and other taurine and indicine breeds. Collectively these results support Mashona being a genetically distinct population relative to breeds more commonly utilized in the US beef industry; such a broad array of genetic diversity suggests there may be substantial allele reservoirs capable of conferring selective advantages to counter negative impacts of climate change.