Genomic insights into the population structure and genetic diversity of Ugandan indigenous cattle

Domestic cattle in Africa can be categorized as either taurine (Bos taurus) or indicine (Bos indicus) based on their domestication histories from the extinct aurochs (Bos primigenius). Close to 150 breeds of indigenous cattle are estimated to exist in Africa and have a complex mixture of B. taurus and B. indicus ancestries. Native cattle in Uganda fall into three broad categories: the Sanga, East African Shorthorn Zebu, and Zenga. There is limited information about the genetics of Ugandan indigenous cattle, despite their representation of nearly 80% of the national herd. In the present study, we describe the genetic diversity and population structure of five native breeds using whole genome sequences of 95 animals. For a comparative context, we included published whole genome sequences of 97 animals in the analysis. Our findings indicate a clear distinction between Zebu, Sanga, and Zenga breeds, with elevated inbreeding and lower genetic diversity levels among the Ugandan breeds. We also observed an introgression of European genetic resources into Ugandan native cattle breeds. Notably, our results suggest existence of two subpopulations within the Nganda breed, a finding that has implications on the conservation efforts of native animal genetic resources. The findings of this study show that indigenous cattle genetic resources in the country are threatened by admixture with imported genetic material and underscore the need for targeted efforts to characterize and conserve them before they are lost to crossbreeding and breed substitution.