Identification of genome diversity in marandi chicken using whole genome sequencing method

 Evaluation and conservation of native chickens as future genomic resources are essential. In this study, genomic diversity of four Marandi breeds was investigated using whole genome sequencing technique.  

 Blood samples were taken from four chickens in East Azerbaijan province, Iran. Whole genome sequencing (paired end sequencing) was done by Illumina Company) Hiseq 2500). Data quality control was performed by FastQC program. Whole genome sequencing data were aligned with genome reference (Gallus_gallus-5.0/galGal5) using MEM algorithmimplemented in burrows wheeler aligner program (BWA). Single nucleotide polymorphisms (SNPs) and small insertions and deletions (INDELs) were identified by the GATK program. Annotation of SNPs and Indels was done using SnpEff program. Genetic diversity of 4 chicken genomes was calculated with VCFtools.   

The short sequences were compared with the reference genome of over 99% and with the mean depth of 7X coverage. In this study, 8.7 million SNPs and 9.1 Indels were identified with the most counts of them in the intron and intergenic regions. The mean of observed and expected heterozygosity percentages for SNPs in four chicken genomes were 0.33 and 0.35, respectively.  

Results from annotation showed that percentage of the silent SNPs (74.64%) is higher than that the nonsynomous SNPs (missense and nonsense) in Marandi chicken genome. The results obtained from this research can be useful for Marandichicken breeding and conservation programs.