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PloS one2021; 16(2); e0247123; doi: 10.1371/journal.pone.0247123

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

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.
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Publication Date: 2021-02-16 PubMed ID: 33592064PubMed Central: PMC7886144DOI: 10.1371/journal.pone.0247123Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research study aimed to distinguish and analyse the characteristics of the Persian Kurdish horse population, in comparison to the Persian Arabian and American Thoroughbred horse populations, by examining genome-wide SNP data.

Methodology

  • The study used genome-wide Single Nucleotide Polymorphism (SNP) data for the comparison.
  • A total of 179 horses – including 58 Kurdish, 38 Persian Arabian, and 83 Thoroughbreds – were examined across 670,796 markers.
  • After conducting quality control and pruning to eliminate linkage disequilibrium between loci, the researchers ended up with 13,554 SNPs across 52 Kurdish, 24 Persian Arabian, and 58 Thoroughbred horses.

Findings

  • The SNP data was used in several analysis techniques including Principal Component Analyses, cluster analyses, and the calculation of pairwise FST.
  • The Persian Kurdish horses were distinct from the Persian Arabian horses in the Principal Component Analyses and other assessments.
  • Both Persian horse breeds (Kurdish and Arabian) were also discernibly different from the Thoroughbred.
  • Pairwise FST – a measure of genetic differentiation – was significantly greater than zero between the two Persian horse breeds but lower than the FST between the Thoroughbred and either Persian breed.
  • Cluster analysis found that Kurdish and Thoroughbred horses fell into distinct genetic clusters. However, the Persian Arabian horses were not in a distinct cluster, suggesting a shared ancestry or recent amalgamation with the Kurdish breed.
  • The level of genetic diversity, as quantified by expected heterozygosity, was highest in the Kurdish horse, followed by the Persian Arabian, and then the Thoroughbred.
  • Analysis of Molecular Variance showed that about 4.47% of genetic variation was present among populations.
  • In terms of inbreeding, the Population-specific inbreeding indices (FIS) were not significantly different from zero in any of the populations. An analysis of individual inbreeding based on runs of homozygosity (ROH) using a larger SNP set indicated greater diversity in both the Kurdish and Persian Arabian horses when compared to the Thoroughbred.

Implications

The results of this research could have potential implications for developing conservation strategies for these horse populations. By understanding the genetic diversity and distinct characteristics of different horse breeds, more informed and effective breeding goals can be set to maintain genetic diversity and the health of the horse populations.

Cite This Article

APA
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

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 16
Issue: 2
Pages: e0247123
PII: e0247123

Researcher Affiliations

Yousefi-Mashouf, Navid
  • MH Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States of America.
Mehrabani-Yeganeh, Hassan
  • Department of Animal Sciences, University of Tehran, Karaj, Iran.
Nejati-Javaremi, Ardeshir
  • Department of Animal Sciences, University of Tehran, Karaj, Iran.
Bailey, Ernest
  • MH Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States of America.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States of America.

MeSH Terms

  • Animals
  • Cluster Analysis
  • Female
  • Genetic Variation / genetics
  • Genomics
  • Genotype
  • Genotyping Techniques
  • Heterozygote
  • Homozygote
  • Horses
  • Linkage Disequilibrium / genetics
  • Male
  • Microsatellite Repeats / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Principal Component Analysis

Conflict of Interest Statement

NYM and HMY, The fund was provided by a private company, Ava Tejarat Saba for non-profit purposes. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

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Citations

This article has been cited 4 times.
  1. Mousavi SF, Razmkabir M, Rostamzadeh J, Seyedabadi HR, Naboulsi R, Petersen JL, Lindgren G. Genetic diversity and signatures of selection in four indigenous horse breeds of Iran. Heredity (Edinb) 2023 Aug;131(2):96-108.
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