Analysis of population structure and genetic diversity of five indigenous African cattle breeds using whole genome sequence data

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 assumed 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 Zebu, and the 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 comparison and contextualization purposes, 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 influx of exotic genetic resources of European descent into these native cattle breeds. Notably, our results show existence of two sub-populations 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 potential admixture with exotic resources and underscore a need for targeted and comprehensive efforts to characterize and conserve these valuable animal genetic resources before they are lost to crossbreeding and breed substitution.