Genetic diversity, population structure and runs of homozygosity in Ethiopian short fat-tailed and Awassi sheep breeds using genome-wide 50k SNP markers

•Selection on the Awassi sheep resulted in significant differentiation from the local Awassi.•Breeds under selection showed higher level of genomic inbreeding.•The highest level of genomic inbreeding observed in Awassi sheep breed.•ROH based genomic inbreeding suggested as a tool to control the level of inbreeding. Improved Awassi sheep from Israel has been used for the improvement of the productivity of Ethiopian short-fat tailed Menz and Wollo sheep breeds through crossbreeding. High density (~50,000) single nucleotide polymorphism (SNP) markers distributed along the ovine genome were analyzed for Menz (n = =34), Wollo (n = =18), local Awassi (n = =24) and improved Awassi (n = =23) sheep breeds to assess genetic diversity and population structure. Proportion of polymorphism was highest for local Awassi (96.2%) followed by the Ethiopian breeds (91.7 to 93.0%). Lowest proportion of polymorphic SNP was found in improved Awassi (84.3%). Expected heterozygosity was high (0.37) for local Awassi followed by the local Ethiopian breeds (0.35 and 0.36) and the improved Awassi (0.35). Highest genetic differentiation measured as fixation index (FST) appeared between local Ethiopian breeds and improved Awassi (FST ~ 0.14) while the two Ethiopian breeds were closely related (FST=0.004). Surprisingly, local Awassi sheep differentiated from improved Awassi at a higher level (FST = 0.09) than it differentiated from Wollo (FST = 0.058) and Menz (FST = 0.065). Principal component, model based structure and neighbor net analysis revealed clustering of populations according to their geographic location and breed development history. Strong selection pressure on the Awassi sheep resulted in significant differentiation from local Awassi, less within population variation, excess monomorphic loci and high level of runs of homozygosity (ROH) based genomic inbreeding. The high level of differentiation between local Ethiopian and improved Awassi supported the use of improved Awassi sheep to improve Menz and Wollo sheep breeds. However, importation of Awassi sheep and mating should consider strategies of controlling the level of inbreeding.