The Study of Genetic Diversity in Khazak Native Chicken Using Whole Genome Sequencing

Objective Indigenous animals are considered as the national treasures and strategic sources of each country. It is essential to preserve and reproduce them. Since no artificial selection has been employed in Iranian native breeds, there is considerable diversity in their genome. Therefore, having detailed information on the animals’ genome can be important for designing breeding plans in the future. The aim of this study was to identify the functional effects of single nucleotide polymorphisms and investigate the genetic diversity in the Khazak chicken ecotype using sequence information of the whole genome. Materials and methods In this study, 17 Khazak chicken samples were sequenced using Next Generation Sequencing (NGS) technique. After preprocessing short sequences using FastQC, Trimmomatic, BWA, Picard software and the GATK program, single nucleotide polymorphisms were identified in GATK program using the UnifiedGenotyper tool. Samtools software was applied to calculate short reads coverage and the percentage of read alignment with the reference genome. The filtering steps of SNPs were performed using Plink software. The genetic diversity within the target population was calculated using the VCFtools program. Results The mean coverage depth for 17 chickens was 6.45. After preprocessing the short sequences, were identified 15,981,176 and 10,552,735 SNPs before and after the quality control, respectively. Functional annotation of the single nucleotide polymorphisms indicated that most of the SNPs are located in the intron and intergenic regions and only 2.8% of them belong to the exon region. The rate of Transition to transversion mutations (Ti / Tv) was 2.43 and the ratio of heterozygous to homozygous SNPs was 3.3 in the Khazak birds, on average. Conclusions The higher number of heterozygous SNPs indicates that there is a high genetic diversity in the Khazak ecotype. Like other Iranian native chickens, the ecotype has the genetic diversity that can be considered a native laying ecotype in the breeding programs.