Abstract
The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calculation of pairwise FST. Both Persian breeds were discriminated from the Thoroughbred. Pairwise FST between the two Persian samples (0.013) was significantly greater than zero and several fold less than those found between the Thoroughbred and Kurdish (0.052) or Thoroughbred and Persian Arabian (0.057). Cluster analysis assuming three genetic clusters assigned the Kurdish horse and Thoroughbred to distinct clusters (0.942 in cluster 2 and 0.953 in cluster 3 respectively); the Persian Arabian was not in a distinct cluster (0.519 in cluster 1), demonstrating shared ancestry or recent admixture with the Kurdish breed. Diversity as quantified by expected heterozygosity was the highest in the Kurdish horse (0.342), followed by the Persian Arabian (0.328) and the Thoroughbred (0.326). Analysis of Molecular Variance showed that 4.47% of the genetic variation was present among populations (P<0.001). Population-specific inbreeding indices (FIS) were not significantly different from zero in any of the populations. Analysis of individual inbreeding based on runs of homozygosity using a larger SNP set suggested greater diversity in both the Kurdish and Persian Arabian than in the Thoroughbred. These results have implications for developing conservation strategies to achieve sound breeding goals while maintaining genetic diversity.
Highlights
The Kurdish horse of Iran is one of the five major Iranian horse breeds
The Kurdish horses clustered in a manner similar to the Thoroughbred, while the Persian Arabian horses had a wider distribution across PC2, where the Kurdish and Persian Arabian clusters were adjacent to one another, with several individuals lying in overlapping regions
With respect to our hypothesis, we found evidence that the Kurdish horse population is distinct from but shares ancestry with the Persian Arabians
Summary
The Kurdish horse of Iran is one of the five major Iranian horse breeds. The other Iranian horse breeds include Caspian, Turkoman, Persian Arabian ( known as Assil) and DareShouri. It is believed that the Nesayee horses brought to the Southwest of Iran became the ancestors of the modern Persian Arabian horses. No formal registry exists for the Kurdish horse, the breed is a well-known landrace, selected for agility, dressage gaits, mountain riding and resistance to harsh environmental conditions. We previously characterized the Kurdish horse from a phenotypic perspective by establishing the breed standards, which describe the ideal characteristics used as selection criteria by breeders [2]
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