Assignment test in Kurdish horse population using SNP chip

Abstract

Introduction: According to the characteristics of Iranian horse breeds and the demand for export, their identification, preservation and reproduction have become important. Kurdish horse is one of the native breeds of Iran, which is distinguished from other native breeds of Iran by having special characteristics. Materials & Methods: In this research, single nucleotide markers (SNP chip) were used to investigate the genetic structure or assignment in a 72 Iranian Kurdish breed horses population. After extracting the DNA of the samples, the genotype was determined using the GGP Equine 70K SNP genomic chip. Quality control of genomic data was done using PLINK v1.07 software. After the quality control steps, PLINK v1.9 Admixture software was used to study the relationship and genetic differentiation between populations, principal component analysis (PCA), Admixture, and phylogenetic relationships. The results of PCA, admixture and phylogeny analyzes were displayed in Python (using Matplotlib library), R (in ggplot2 package) and FigTree environments, respectively. Recent and past effective population sizes were estimated using SNeP software, which uses average linkage disequilibrium between different SNP pairwise intervals. The linkage disequilibrium pattern of the entire Kurdish horse genome was calculated using the r2 statistic. Results: The results of genomic linkage disequilibrium (LD) analysis indicated a relatively high reduction of the linkage pattern between 0-50 kb intervals (0.2 ≥ r2 ≥ 0.1) in this population. For the assignment test, SNPs with minimum allelic frequency (MAF) less than 50%, samples with more than 10% unhealthy genotype and SNPs out of Hardy-Weinberg equilibrium (probability less than 10-6) were excluded. Conclusion: Therefore, according to the pattern observed from the results of this study and according to the origin of different Iranian horse populations (with the exception of the Kurdish population), it is possible to divide the Iranian horse populations into two categories of horses on the eastern and southern coasts of the Mazandaran Sea. (Turkmen and Caspian) and the horses of southwest Iran (Asil and Dareh Shuri). Also, due to the decreasing trend in the effective size over the generations, it is necessary to design appropriate programs to protect the Kurdish horse breed.