Assessment of Genetic Diversity and Phylogenetic Relationship of Iranian Indigenous Chickens Based on Mitochondrial D-Loop Sequences

In the present study for evaluation of genetic variability within and between Iranian native fowls, thirty nine blood samples were randomly collected from native fowls breeding stations of west Azarbayjan, Khorasan, Fars, Mazandaran, Yazd and Esfahan provinces. Inorder to compare the obtained results with other Asian, African and European breeds the D-loop sequences of mtDNA taken from GenBank. Total DNA of the samples was extracted by salting out procedure and was used as a template for amplification and sequencing of D-loop region of mtDNA. Sequence analysis of the 1231-2 bp D-loop region in all samples revealed a total of 16 haplotypes with 14 polymorphic sites. Analysis of molecular variance (AMOVA) was carried out based on Kimura method .The Fixation index values using kimura-2 parameter method ranged from -0.157 to 0.37763. The variation within and between the populations was estimate as (81.05 and 18.95, respectively). The genetic distance between Esfahan and West Azarbayejan, Esfahan and Fars, Esfahan and Khorasan, Esfahan and Mazandaran, Esfahan and Yazd, Fars and khorasan, Fars and Yazd populations were significantly different (p