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Home / Equine Research Bank / PLoS One / Genome-wide analysis of population structure, effective popu...
PloS one2024; 19(3); e0299109; doi: 10.1371/journal.pone.0299109

Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses.

Abstract: Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of principal component (DAPC) and model-based method (STRUCTURE) were employed. The results of the population analysis clearly demonstrated a distinct separation of native and exotic horse breeds and clarified the relationships between studied breeds. The effective population size (Ne) for the last six generations was estimated 54, 49, 37, 35, 27 and 26 for the Caspian, Kurdish, Arabian, Turkmen, Akhal-Teke and Fell pony breeds, respectively. The Caspian breed showed the lowest LD with an average r2 value of 0.079, while the highest was observed in Fell pony (0.148). The highest and lowest average observed heterozygosity were found in the Kurdish breeds (0.346) and Fell pony (0.290) breeds, respectively. The lowest genomic inbreeding coefficient based on run of homozygosity (FROH) and excess of homozygosity (FHOM) was in the Caspian and Kurdish breeds, respectively, while based on genomic relationship matrix) FGRM) and correlation between uniting gametes) FUNI) the lowest genomic inbreeding coefficient was found in the Kurdish breed. The estimation of genomic inbreeding rates in the six breeds revealed that FROH yielded lower estimates compared to the other three methods. Additionally, the Iranian breeds displayed lower levels of inbreeding compared to the exotic breeds. Overall, the findings of this study provide valuable insights for the development of effective breeding management strategies aimed at preserving these horse breeds.
Copyright: © 2024 Bazvand et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Publication Date: 2024-03-05 PubMed ID: 38442089PubMed Central: PMC10914290DOI: 10.1371/journal.pone.0299109Google 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 aimed at understanding the population structure, effective population size, genetic diversity, and genomic inbreeding among diverse horse breeds. The study involved Iranian native horses and some exotic breeds, and provided insights that may aid in the development of effective horse breeding management strategies.

Study Methodology

  • The research focused on several different horse breeds including Iranian natives like Caspian, Turkmen, Kurdish and exotic ones like Arabian, Fell pony, and Akhal-Teke.
  • The study utilized various statistical population analysis techniques in its methodology, which include principal component analysis (PCA), discriminant analysis of principal component (DAPC), and a model-based method called STRUCTURE.

Findings and Observations

  • From the population analysis, a clear and distinct separation between the native and exotic horse breeds was observed.
  • Depending on the breed, the estimated effective population size (Ne) for the last six generations varied: The Caspian breed had the highest Ne at 54 while the Fell pony breed registered the lowest at 26.
  • In terms of linkage disequilibrium (LD), the Caspian breed demonstrated the lowest level, while the Fell pony had the highest LD.
  • Regarding genetic diversity, the study determined heterozygosity levels in the breeds. The Kurdish breed exhibited the highest observed heterozygosity while the Fell pony had the lowest.

Inbreeding Evaluations

  • The research also estimated genomic inbreeding rates in the six studied horse breeds. For this, four different methods were applied: run of homozygosity (FROH), excess of homozygosity (FHOM), genomic relationship matrix (FGRM), and correlation between uniting gametes (FUNI).
  • The Caspian and Kurdish breeds had the lowest genomic inbreeding coefficient, according to FROH and FHOM, respectively. Based on FGRM and FUNI methods, the Kurdish breed also had the lowest genomic inbreeding coefficient.
  • Overall, the FROH method yielded lower estimates compared to the other methods, and the Iranian breeds exhibited lower levels of inbreeding compared to the exotic breeds.

Implications and Conclusions

  • The results of this study are of particular interest for developing effective breeding management strategies, especially in efforts towards preserving these horse breeds.
  • Knowing the level of genetic diversity and inbreeding can help in maintaining and improving a breed’s health and vitality.

Cite This Article

APA
Bazvand B, Rashidi A, Zandi MB, Moradi MH, Rostamzadeh J. (2024). Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses. PLoS One, 19(3), e0299109. https://doi.org/10.1371/journal.pone.0299109

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 19
Issue: 3
Pages: e0299109
PII: e0299109

Researcher Affiliations

Bazvand, B
  • Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran.
Rashidi, A
  • Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran.
Zandi, M B
  • Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran.
Moradi, M H
  • Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.
Rostamzadeh, J
  • Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran.

MeSH Terms

  • Horses / genetics
  • Animals
  • Humans
  • Inbreeding
  • Population Density
  • Iran
  • Genomics
  • Discriminant Analysis

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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