The taxonomy of Alectoris chukar (A. chukar) has been a complex debate with different classifications and revisions suggested based on their morphology, geographical distribution and chromosome number. In Pakistan the Chukar partridge (A.chukar)), is an important member of Phasianidae family, however a scarce molecular data is reported that urged us to investigate its genetic diversity and phylogeny using mitochondrial DNA, Cyt-b and Cox1 genes. A total of 749bp of Cox1 and 472 bp of Cyt-b complete coding regions of both genes were amplified by PCR followed by sequencing. The sequences were aligned and edited using Bio-Edit software and single nucleotide polymorphisms (SNPs) were identified. The boot strapped Neighbor joining tree constructed from MEGA7 explained the genetic relationships of A.chukar with related members of Phasianidae family. The phylogenetic analysis also showed the genetic positioning of A. chukar with respect to other different reported species as well. The study gave us useful genomic information about genetic diversity in A. chukar and its phylogenetic relationships with related taxa, emphasizing on need of execution of conservation strategies to protect this unique genetic resource of Pakistan.
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