Genome-wide analysis of population structure and genetic diversity in two Ethiopian native sheep populations

Indigenous Ethiopian sheep inhabit diverse environmental conditions and hold distinct morphological traits, including variations in tail phenotypes. Characterizing their genetic diversity is crucial for developing appropriate breeding and conservation schemes. The current study aimed to determine the genetic diversity and population structure of two underrepresented indigenous sheep populations in Ethiopia: Selale and Semien. A total of 48 whole blood samples were collected randomly from the 24 Selale and 24 Semien sheep. Publicly available single nucleotide polymorphism genotype data from five Ethiopian sheep populations (Arsi-Bale, Menz, Blackhead Somali, Horro, and Adilo) were included in the analysis. Additionally, for an even broader perspective, four breeds from Asia and other parts of Africa (Afshari, Egyptian Barki, Red Maasai, and Indian Garole) were used to evaluate the genetic connections of the study populations. The average genetic diversity (expected heterozygosity) ranged from 0.325 for Ari-Bale to 0.362 for the Selale sheep, with a mean of (H_E = 0.344) across all populations. Estimates of genetic differentiation among sheep populations in Ethiopia ranged from 0.019 between Selale and Horro sheep to 0.077 between Semien and Arsi-Bale sheep. The analysis of molecular variance indicated that 94.25 % and 3.56 % of the genetic differentiation were attributable to variances within and among populations, respectively. Principal component and admixture analyses revealed three distinct genomic backgrounds of indigenous sheep populations in Ethiopia, consistent with their tail morphology and ecological distribution: long fat-tailed, short fat-tailed, and fat-rumped sheep. These findings can help formulate strategies for sustainable genetic improvement, conservation, and utilization of indigenous sheep populations.