M. H. Moradi - Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak ۳۸۱۵۶-۸-۸۳۴۹, Islamic Republic of Iran.
S. H. Phua - Centre for Reproduction and Genomics, AgResearch Invermay, Mosgiel, New Zealand.
N. Hedayat - Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Islamic Republic of Iran.
M. Khodaei-Motlagh - Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak ۳۸۱۵۶-۸-۸۳۴۹, Islamic Republic of Iran.
M. Razmkabir - Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Kurdistan, Sanandaj, Islamic Republic of Iran.

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 ۰.۰۵۴ and ۴.۷۱۵ respectively, indicating a low mitochondrial genetic differentiation and high gene flow between two sheep breeds. The Analysis of Variation (AMOVA) showed that around ۹۷% 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 H۱ and H۳, were present at higher frequencies in both breeds. Haplotyes H۵, H۶, H۷, H۸ and H۹ were found as population-specific in the Zel, and haplotype H۲ only occurred in Lori-Bakhtiari breed. The existence of two common Haplotypes (H۱ and H۳) 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.

genetic diversity, Haplogroups, Mitochondrial genome, Phylogenetic study, Sheep evolution