Genomic diversity and population structure analysis reveal few genetic differences among Ethiopian indigenous sheep populations

African sheep, like other domestic sheep, are domesticated from the Asiatic mouflon (Ovis orientalis). They entered the continent through the North and the Horn of Africa regions following maritime and terrestrial trading routes. Ethiopia is one of the main entry points of various plant and animal domesticates into Africa. It is characterised by diverse agro-ecologies, ancient human ethnic diversity and the presence of indigenous sheep breeds/populations of unprecedented morphological diversity (e.g. tail types). Here, we investigate the genome diversity and population structure of 146 unrelated animals from 11 Ethiopian indigenous sheep populations. DNA was extracted from ear tissue punches and genotyped with the Illumina Ovine 50K SNP BeadChip assay. Sheep populations from The Caribbean, Europe, Middle East and China as well as from western, northern and southern Africa were included to clarify the genetic history of origin, introduction and dispersal of the species into Ethiopia. Principal component analysis (PCA), clearly separated all Ethiopian sheep from the other populations. Population structure and phylogenetic (neighbour-joining tree) analysis subdivided the Ethiopian indigenous sheep into three genetic clusters corresponding to their tail morphology (rump fat-tailed, short fat-tailed and long fat/thin-tailed population). It supports a common genetic ancestry for populations of each tail type in the country. Genetic distances among the Ethiopian populations were positively correlated with geographic distances (Mantel test, P < 0.001, r = 0.465) and the highest genetic diversity was recorded in the fat-tailed (short, rump and/or long fat-tailed) close to the Bab-el-Mandeb strait. However, despite their distinct morphology and separate geographic distribution, little genetic differentiation between Ethiopian populations are observed. This is most likely a consequence of their ancient and modern intermixing following their introduction into the country.