Identification of genome diversity in different breeds of Iranian native sheep using the whole genome sequencing method

Iran is considered to be one of the oldest centers of domestication and breeding of livestock and poultry species in the world. Currently, different ecotypes of indigenous sheep are kept in different geographical regions of the country, which have obvious differences from each other in terms of appearance and production characteristics. So far, there has not been a comprehensive study on the whole genome level to identify the genetic diversity of native Iranian sheep. Therefore, the aim of this study is to identify the genomic characteristics of these native reserves in order to organize appropriate programs for their exploitation and protection

In this study, the whole genome sequences of 29 native Iranian sheep were downloaded from the NCBI database and analyzed. Whole genome sequencing of the studied data has been done by Hiseq2000 and Hiseq X Ten sequencer devices. Quality control of raw data sequences was done by FastQC program. To align the sequence data with the sheep reference genome (Oar v.4.0, https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.2), the BWA-MEM algorithm used in the BWA software package was used. Picard program was used to remove PCR duplicates from mapping outputs. The alignment outputs with the reference genome were processed in two stages, including re-alignment of deletions and small insertions and recalibration of the base quality score using the GATK program. The average coverage depth and alignment percentage for alignment output with the reference genome were calculated using depth and flagstat commands used in samtools software. Single nucleotide polymorphisms (SNPs) were identified by the UnifiedGenotyper tool used in the GATK program. Nucleotide diversity values and genomic inbreeding coefficient were calculated based on homozygous SNPs for each individual using the het command used in the VCFtools program.

The average coverage depth of the used data in this study was 18.39 X. The average percentage of alignment of short sequences with the sheep reference genome was 99.89%. The values of genomic inbreeding coefficient in Iranian native sheep breeds ranged from 0.01 to 0.12. The lowest value of genomic inbreeding coefficient was observed in the genome of Mughani sheep (0.01) and the highest value of inbreeding coefficient was observed in the genome of Afshari sheep. Also, the average values of observed and expected percentage of heterozygosity calculated for single nucleotide polymorphisms in the genome of Iranian native sheep ecotypes ranged from 20.67 to 23.06 and 32.415 to 32.421.