Invetigation of genetic structure of Khalkhali goat using mitochondrial genome

Local species are considered as a part of national capital and strategic recourses. Due to significant decline of their population, identification, preservation and reproduction of local breeds is very important. In this study D-loop region of mtDNA was used for analyzing genetic diversity, phylogenetic and genetics structure of Khalkhali goat population. Blood samples were collected from 100 Khalkhali goats and, genomic DNA was extracted using DNA extracting kit and amplified with specific primers. Then, genotyping were performed using SSCP method and were sequenced through detection of different pattern. mtDNA sequences of other species were collected from NCBI (as outgroups sequences) and analyzed by using bioinformatics software’s. In total 62 mutations were identified in 126 sequences that cause 37 haplotype. Haplotype diversity, nucleotide diversity between species were 0.915 and 0.069 respectively. Genetic diversity and haplotype diversity of Khalkhali goat was 0.008 and 0.834 respectively, which indicated low genetic diversity in this breed. The comparison between khalkhali goat and others haplotypes showed that khalkhali goat were located on Haplogoup A.