Analysis of SNP Chip 70k Genomic Data to Identify Loci Related to Differentiation of Caspian and Kurdish Horses using Selection Sweep

 Selection in animal populations to increase the frequency of ideal alleles causes of remaining some signs in the animal genome, which are usually associated with important traits. Today, with developments in next-generation sequencing and easier access to animal genomic information, some models have been proposed to identify selective signatures based on allelic frequency and haplotype blocks. This research aimed to identify the selective signatures in two horse breeds of Caspian and Kurdish using a k70 SNP chip.

 In this research blood samples from 35 Caspian and 31 Kurdish horses were collected. After DNA extraction and sequencing (by Illumina company), Quality control of the data was performed for minimum allele frequency (PMAF<0.05), genotyping rate (PGENO < 0.5), and deviation from Hardy-Weinberg equilibrium (PH-W<1 ͯ 10-6). Then the theta (θ) test and ensemble site were used for identifying selective signatures and the positions of snaps respectively, and finally, the genes related to these positions were identified.

 After quality control of data and integration of genomic data of two populations based on R package protocols, 61 horses with 52,650 SNPs remained for the rest analysis. Finally, Fst statistical test based on unbiased estimator theta method 31 differentiating markers of the two studied horse breed were identified

The results showed that Caspian and Kurdish horse breeds belong to two separate groups. The Kurdish horse breed has more diversity and variety than the Caspian. The most important genes associated with significant SNPs were INPP5F, HPSE2, R3HCC1, DOCK3, ITGB6, GM6B, PHEX, WDR13, LRCH2, GRIA3 and THOC2. Most of the identified genes were associated with intercellular exchanges, muscle contractions, immunity, membrane support, DNA stability, and the nervous system.