Genetic diversity of Hajar1 and Hajar2 local Saudi chicken lines using mitochondrial DNA D-loop markers

This study was conducted to assess genetic diversity of Hajar1 and Hajar2 local Saudi chicken lines using mitochondrial DNA (mtDNA) D-loop partial sequences. One hundred blood samples were obtained equally from Hajar1 and Hajar2 Saudi chicken lines as 50 samples from each line. The D-loop region was partially amplified from genomic DNA with a conserved primer set, and the fragments were sequenced. Eight published reference mtDNA sequence data from the GenBank were used for comparisons, and multiple alignments were performed. The most common haplotype was assigned as a basic sequence for comparing within each line. Entropy plot and conserved region analysis were performed. Genetic distances and neighbour-joining (NJ) phylogenetic trees were estimated. The results indicated haplotype variations within and between local Saudi chicken lines, which could explain the phenotypic variation reported earlier. A close genetic relationship was shown between the Saudi local chicken lines. Unique conserved regions and nucleotide substitutions were observed between the two lines. Both lines have a close relationship with the reference Asian local chicken population, especially local Chinese and Indian chicken breeds. The current results are considered the first report of mtDNA sequence diversity for Hajar1 and Hajar2 lines. Further detailed molecular genetic studies of both lines are indispensable to genetic conservation and development.Keywords: chicken population, diversity, D-loop, Hajar1, Hajar2, mtDN