Identification of Genomic Differences Resulting from Selection in Iranian Kurdish and Turkmen Horse Breeds Using Single Nucleotide Polymorphisms.

Background: Breakthroughs in genomic technologies have enabled the formulation of methods to identify genomic variation in domestic animal species. Detection of the variation is necessary because it is associated with breed characteristics and economic importance in domestic animal genetics. Objectives: This study aimed to identify the genomic regions in Turkmen and Kurdish horse breeds that have been the target of different selections over many years. It also sought to locate the genes and Quantitative trait loci (QTL) in these regions that contributed to the differentiation of these two breeds or the distinguishing traits within them breeds. Materials and Methods: In this research, the genomic differences between the Iranian Turkmen and Kurdish horses were identified using 70kb SNP markers. For this purpose, each breed's 68 Turkmen and 32 Kurdish horses were selected and genotyped. After data quality control and population structure investigation, 82 horses with 49,578 single nucleotide markers were used to search for the identification of genomic differences. Two statistical tests, fixation index (Fst) and cross-population extended haplotype homozygosity (XP-EHH), were used to identify genomic differences between populations. Results: Using the Fst test, 4 genomic regions on chromosomes 5, 12, 29, and 30, whose theta is in the top 99.9% percentile of theta value of the experimental distribution of theta, were identified as population differentiation regions in both breeds. To identify differences caused by selection in these regions, the extended haplotype homozygosity test and the length of gene linkage disequilibrium were used. The analysis showed that chromosomes 5, 12, and 29 in Kurdish horses and chromosome 30 in Turkmen horses had differences caused by selection. The genes that played a role in the nervous system, cell metabolism, immune system, cell division, and gene regulation and expression were identified in these regions. The XP-EHH test identified 5 genomic regions on chromosomes 4, 5,9,10 and 11 as candidate regions for genomic differentiation in both populations. In each genomic region, several genes with different functions were identified. Several QTLs were identified on chromosome 4 in Turkmen horses, which are associated with reproductive traits in horses. A QTL with susceptibility to insect bites was identified on chromosome 11 of Kurdish horses. Using both mentioned statistical tests, regions on chromosome 5 were identified as candidate regions for selection in both breeds. Conclusion: Selection signatures in horse genomes indicate that natural and artificial selection have significantly influenced their genetic diversity. This data can enhance the understanding of horses' evolutionary past and refine breeding initiatives focused on enhancing their economic, functional, and biological traits. Examining selection signals offers essential resources for preserving genetic variety and improving productivity in equine breeding.