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BMC genomics2024; 25(1); 772; doi: 10.1186/s12864-024-10682-8

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.

Abstract: The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds. Results: HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20). Conclusions: Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.
© 2024. The Author(s).
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Publication Date: 2024-08-08 PubMed ID: 39118059PubMed Central: PMC11308356DOI: 10.1186/s12864-024-10682-8Google 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 article is about a study examining genetic diversity and the effect of selection pressures in the Icelandic horse and Exmoor pony breeds, two ancient types of horses known for their resilience to harsh environments but which have also experienced significant genetic bottlenecks.

Research Goal and Methodology

  • The overall goal of the research was to study the genetic diversity in the Icelandic horse and the Exmoor pony, two distinct breeds that have experienced significant genetic ‘bottlenecks’. This refers to a sharp reduction in population size leading to genetic diversity loss.
  • The researchers looked at the expected and observed heterozygosity – measures of genetic diversity – and the effective population size (Ne). They also examined runs of homozygosity (ROH), sequences where both of a pair of chromosomes are identical, to compare genomic inbreeding and signatures of selection – the impact of evolutionary processes – in the breeds.

Results of the Research

  • According to the results, the expected heterozygosity was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with the observed heterozygosity of 0.34 for both breeds. This suggests comparable levels of genetic diversity within both breeds.
  • The effective population size for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies, based on genomic data. This suggests that the Icelandic horses have a larger pool of breeding individuals than the Exmoor ponies.
  • The genomic inbreeding coefficient, a measure of the degree to which individuals within a population are related, varied from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony. This suggests more inbreeding among Exmoor ponies than Icelandic horses.

Unique Findings and Conclusion

  • Several ROH islands associated with performance were identified in Icelandic horse, indicating locations in their genome positively selected for specific performance traits. The identified ROH islands in Exmoor ponies were associated with traits such as coat colours, the immune system, and fertility.
  • While genetic diversity in Icelandic horses is deemed acceptable, a critically low genetic diversity was estimated for the Exmoor pony, suggesting the Exmoor pony breed may need intervention to maintain its genetic health.
  • The research concluded that the study’s findings provide insight into the genomic regions under selection pressure in a gaited performance horse breed, and various adaptive traits in small-sized native horse breeds. Thus, the findings could contribute to the preservation of genetic diversity and population health in these equine populations.

Cite This Article

APA
Sigurðardóttir H, Ablondi M, Kristjansson T, Lindgren G, Eriksson S. (2024). Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies. BMC Genomics, 25(1), 772. https://doi.org/10.1186/s12864-024-10682-8

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 25
Issue: 1
Pages: 772

Researcher Affiliations

Sigurðardóttir, Heiðrún
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden. heidrun.sigurdardottir@slu.se.
  • Faculty of Agricultural Sciences, Agricultural University of Iceland, Hvanneyri, Borgarbyggð, 311, Iceland. heidrun.sigurdardottir@slu.se.
Ablondi, Michela
  • Department of Veterinary Science, University of Parma, Parma, 43126, Italy.
Kristjansson, Thorvaldur
  • Faculty of Agricultural Sciences, Agricultural University of Iceland, Hvanneyri, Borgarbyggð, 311, Iceland.
Lindgren, Gabriella
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden.
  • Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, 3001, Belgium.
Eriksson, Susanne
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden.

MeSH Terms

  • Horses / genetics
  • Animals
  • Genetic Variation
  • Selection, Genetic
  • Homozygote
  • Iceland
  • Inbreeding
  • Genomics / methods
  • Polymorphism, Single Nucleotide
  • Heterozygote
  • Breeding
  • Genetics, Population

Conflict of Interest Statement

The authors declare competing interests concerning the commercial applications of the current study. GL is a co-inventor of a patent application concerning commercial testing of the DMRT3 mutation. The stated patent does not restrict research applications of the method. None of the other authors have any competing interests.

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