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Home / Equine Research Bank / Anim Genet / Population structure and genomic footprints of selection in ...
Animal genetics2022; 53(5); 627-639; doi: 10.1111/age.13243

Population structure and genomic footprints of selection in five major Iranian horse breeds.

Abstract: The genetic structure and characteristics of Iranian native breeds are yet to be comprehensibly investigated and studied. Therefore, we employed genomic information of 364 Iranian native horses representing the Asil (n = 109), Caspian (n = 40), Dareshuri (n = 44), Kurdish (n = 95), and Turkoman (n = 76) breeds to reveal the genetic structure and characteristics. For these and 19 other horse breeds, principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches were applied to investigate and compare their genetic structure. Additionally, three haplotype-based methods including haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length were applied to trace genomic footprints of selection of Asil, Caspian, Dareshuri, Kurdish, and Turkoman groups. Then, the Mahalanobis distance based on the negative-log10 rank-based P-values was estimated based on the haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length values. Asil, Caspian, Dareshuri, Kurdish, and Turkoman can be categorized into five different genetic clusters. Based on the top 1% of Mahalanobis distance based on the negative-log10 rank-based P-values of SNPs, we identified 24 SNPs formerly reported to be associated with different traits and >100 genes undergoing selection pressures in Asil, Caspian, Dareshuri, Kurdish, and Turkoman. The detected QTL undergoing selection pressures were associated with withers height, equine metabolic syndrome, overall body size, insect bite hypersensitivity, guttural pouch tympany, white markings, Rhodococcus equi infection, jumping test score, alternate gaits, and body weight traits. Our findings will aid to have a better perspective of the genetic characteristics and population structure of Asil, Caspian, Dareshuri, Kurdish, and Turkoman horses as Iranian native horse breeds.
© 2022 Stichting International Foundation for Animal Genetics.
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Publication Date: 2022-08-02 PubMed ID: 35919961DOI: 10.1111/age.13243Google 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.

This research focuses on understanding the genetic structure and unique traits of five Iranian native horse breeds—namely Asil, Caspian, Dareshuri, Kurdish, and Turkoman—using genomic data. The findings reveal distinct genetic clusters for each breed and identify different traits linked to specific genes.

Research Methodology

  • The researchers studied the genomic information of 364 Iranian native horses representative of the five breeds: Asil, Caspian, Dareshuri, Kurdish, and Turkoman.
  • They used principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches to investigate and compare the genetic structure of these horse breeds with 19 other horse breeds.
  • Three haplotype-based methods (haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length) were employed to trace the genomic footprints of selection among the five Iranian groups.
  • The Mahalanobis distance, a statistical measure, was calculated based on the negative-log rank-based P-values of the haplotype-based methods. This helped determine the different genetic clusters among the breeds.

Findings and Results

  • The five Iranian breeds could each be categorized into separate genetic clusters, indicating specific genetic structures for each breed.
  • By analyzing the top 1% of Mahalanobis distance based on the negative-log rank-based P-values of single nucleotide polymorphisms (SNPs), they identified 24 SNPs that were found to be associated with different traits.
  • Over 100 genes were detected that were undergoing selection pressures among the five horse breeds.
  • The identified quantitative trait loci (QTL) affected by selection pressures were linked with traits such as withers height (the measurement from the ground to the highest point on a horse’s shoulder), equine metabolic syndrome, overall body size, sensitivity to insect bites, guttural pouch tympany (a condition affecting the respiratory system), white markings, Rhodococcus equi infection (a bacterial infection), jumping test score, alternate gaits, and body weight.

Significance and Impact

  • This research helps provide a comprehensible understanding of the genetic characteristics and population structure of these Iranian native horse breeds.
  • The identified genes and the traits they are associated with can provide valuable insights for breeding and horse health management, particularly for the five studied breeds.
  • The findings will also possibly contribute to developing preservation strategies for these native breeds, protecting their genetic diversity for future generations.

Cite This Article

APA
Salek Ardestani S, Zandi MB, Vahedi SM, Janssens S. (2022). Population structure and genomic footprints of selection in five major Iranian horse breeds. Anim Genet, 53(5), 627-639. https://doi.org/10.1111/age.13243

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 53
Issue: 5
Pages: 627-639

Researcher Affiliations

Salek Ardestani, Siavash
  • Department of Animal Science, University of Zanjan, Zanjan, Iran.
Zandi, Mohammad Bagher
  • Department of Animal Science, University of Zanjan, Zanjan, Iran.
Vahedi, Seyed Milad
  • Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada.
Janssens, Steven
  • Department Biosystems, Center Animal Breeding and Genetics, KU Leuven, Leuven, Belgium.

MeSH Terms

  • Animals
  • Bayes Theorem
  • Genome
  • Genomics
  • Haplotypes
  • Horses / genetics
  • Iran
  • Polymorphism, Single Nucleotide

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