Study population structure in Iranian Arab horse breed by principal component analysis (PCA) and discriminant analysis of principal components (DAPC) methods using genomic data

The preservation and reproduction of native animal species in any country is of considerable value and importance. Iran has native horse breeds that have deep roots in Iranian culture and civilization, so their protection is very necessary. There are various lineages in Iranian Arab horse populations that are usually classified based on morphological and genetic characteristics. The most important lineages include Kohailan, Hamdani, Seglavy, Jolfan, Shuiman, Abyan, Khersan, Hedban or hadian, Malihe, Nasmani, and Vadne. The aim of this study was to use two methods, principal component analysis (PCA) and discriminant principal component analysis (DAPC), to investigate the population structure of Iranian Arabian horses using SNP markers. For this purpose, ۱۰۹ Iranian Arabian horses from the Hamdani(۱۹), Kohailan (۹), Abyan(۱۳), Seglavy(۱۲), Khersan (۵۳) and Shuiman (۳) lineages were sampled. These lineages were identified based on information from the Arabian Horse Pedigree Book of the Islamic Republic of Iran Equestrian Federation. The samples were genotyped using Illumina SNP ۴۰k chips. Data quality control steps were performed using Plink ۱.۹ software and none of the samples were deleted, but at maf ۰.۰۳ we saw the deletion of ۲۳۴۷ SNPs. Then, Python software was used to analyze the data. The results showed that in both analysis methods, the Khersan and Shuiman lineages were completely separated from other lineages, and the Abyan and Kohailan lineages were clustered close to each other, and the Seglavy and Hamdani lineages were also clustered close to each other, and DAPC provided a better picture of the relationship between lineages, which was observed using a Box plot between lineages. Given the small number of samples from different lineages such as Shuiman and the unavailability of phenotypic information of the samples, It is expected that in the future, with this information in hand, more extensive research will be able to be conducted on the Iranian Arabian horse breeds.

کلیدواژه ها:

population structure ، iranian arab horse ، PCA and DAPC methods ، SNP markers