The archaeological evidence suggests that Iran has been one of the first origins of sheep domestication in the world. This study aims to investigate the genetic diversity of indigenous Iranian sheep breeds using mitochondrial DNA (mtDNA) and to explore the evolutionary history of sheep domestication in Iran. Single Nucleotide Polymorphism (SNP) markers in the control region of mtDNA were used to genotype the unrelated sheep samples of Zel and Lori-Bakhtiari breeds which were collected from or near the center of the sheep domestication, using the Sequenom MassARRAY platform. Phylogenetic analysis of the mitochondrial SNPs classified all animals into either of two haplogroups A and B. The population differentiation (FST) and gene flow (Nm) statistics were 0.054 and 4.715 respectively, indicating a low mitochondrial genetic differentiation and high gene flow between two sheep breeds. The Analysis of Variation (AMOVA) showed that around 97% of the total genetic diversity is distributed within the two breeds. Further analysis using SNP haplotyping identified nine different haplotypes within the animals; eight haplotypes were present in the Zel, while only four were seen in the Lori-Bakhtiari breed. Two haplotypes, designated H1 and H3, were present at higher frequencies in both breeds. Haplotyes H5, H6, H7, H8 and H9 were found as population-specific in the Zel, and haplotype H2 only occurred in Lori-Bakhtiari breed. The existence of two common Haplotypes (H1 and H3) in the animals suggest that the two Iranian breeds from strikingly different geographical regions, may share a common ancestry, and these haplotypes could be the origin haplotypes while the population specific haplotypes developed later.
