Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations

Authors

Navid Yousefi-Mashouf, University of Kentucky
Hassan Mehrabani-Yeganeh, University of Tehran
Ardeshir Nejati-Javaremi, University of Tehran
Ernest Bailey, University of Kentucky
Jessica L. Petersen, University of Nebraska-LincolnFollow

ORCID IDs

Navid Yousefi-Mashouf

Document Type

Article

Date of this Version

2-1-2021

Citation

Yousefi-Mashouf N, Mehrabani-Yeganeh H, Nejati-Javaremi A, Bailey E, Petersen JL (2021) Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations. PLoS ONE 16(2): e0247123. https:// doi.org/10.1371/journal.pone.0247123

Comments

CC-BY

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 F_ST. Both Persian breeds were discriminated from the Thoroughbred. Pairwise F_ST 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 (PIS) 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.