Genome-Wide San for Detection of Runs of Homozygosity in Iranian Indigenous Sheep Breeds

Sheep are considered one of the essential livestock with the high ability to adapt to different climates, and a breed diversity was observed in Iran. As a result of different selections, some genomic regions have acquire high purity called Runs of Homozygosity (ROH). By examining these regions in the genome of sheep, the goals of selection in these breeds can be followed and the genes present in these regions can be identified.

For this purpose, the whole-genome sequencing data from 28 samples of Iranian sheep, including Afshar, Ghezel, Karakul, Moghani, Makui, Baluchi, Gray, and Shal breeds, were downloaded from the NCBI database. After quality checking and trimming, high-quality reads were aligned to the sheep reference genome by BWA software. Then the variants were identified and filtered using VCFtools software, a VCF file containing information related to SNPs was created for more analysis. At the end of the analysis, homozygous strands were extracted, and finally, the genes related to these regions were identified.

Based on the results of PCA, the samples related to Iranian sheep breeds were divided into three categories, the first group includes the Karakul and Baluchi breeds (KB), the second group includes the Moghani and Makui breeds (MM), and the third group includes the Shal, Ghezel, Afshari and Gray breeds (SGAG). According to the results of the analysis, ROH areas for KB, MM, and SGAG populations have 419 (52.375 areas per person), 139 (23.17 areas per person), and 876 (62.57 areas per person) ROH areas, respectively. Also, 6 and 17 common ROH (at least two samples) were identified in KB and SGAG populations, respectively. We could not find a common ROH for the MM population. Annotating the sharing ROHs leads to identifying 99 and 173 protein-coding genes within these genomic regions for the KB and SGAG populations, respectively. The results of gene ontology analysis showed that most of these genes are involved in processes such as energy and fat metabolism (FLCN, ELOVL3, STK3, SREBF1, and NCOR1) as well as the growth and development of muscle tissue and meat quality (MYL6 and TMOD1).

According to the results of this study, it could be concluded that there is a high level of diversity and crossbreeding in the native sheep breeds that could be used for different breeding goals and producing breeds with appropriate production. On the other hand, the candidate genes identified in this research also accelerate the time to achieve breeding goals in these breeds.