محمد حسین مرادی

Abstract The lack of complete pedigrees and phenotypic records affect the accuracy of genetic evaluation and consequently the efficiency of breeding programs. The assignment of an individual to the true population of origin is one of the most appealing opportunities to exploit genomic data for practical use in a variety of biological contexts. The aim of this study was to identify the minimum number of informative SNPs from high-throughput genotyping data in Iranian sheep breeds seeking to identify small panels of genetic markers that can be used to trace the breed of unknown sheep samples. Individuals of Zel (47), Lori-Bakhtiari (47), Afshari (41), Moqani (35), Qezel (35) and a wild-type (12) Iranian sheep breed were genotyped using Illumina OvineSNP50K BeadChip. Animals with genotypic call rate more than 95% (207 samples) and the SNPs in Hardy-Weinberg equilibrium (p>10 -6 ) and displaying minor allele frequency (MAF) more than 5% across all the 6 populations were selected for further analysis. Before analyzing the data, the principal component analysis (PCA) was used to determine how the animals allocated to the groups and the degree of divergence between samples. The results revealed that the first two principal components (PC1 and PC2) explained 35% and 17% of the variance respectively. We found that PC1 separated out the two domestic and wild sheep breeds and all domestic breeds were separated from each others for PC2. The genetic distance between different breeds was calculated using FST, Reynold and Mahalanobis methods and the results showed that the closest distance between domestic breeds was obtained between Moqani-Qezel, while the greatest one was observed between Afshar-LoriBakhtiati and also Afshari-Zel. Furthermore, the closet distance between wild-type sheep breed and other domesticated breeds was observed for Zel, the only thin tail sheep breeds in Iran, that can support the hypothesis that the first domesticated sheep were thin tailed and fat tail