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BMC genomics2023; 24(1); 35; doi: 10.1186/s12864-023-09116-8

Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health.

Abstract: Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genomic regions under selection for the population-specific traits, gait, black coat colour, and hoof quality. Other global breeds were used to identify regional-specific signatures of selection. Results: We first identified the most significant selection peak for the Wushen horse in the region on ECA23 harbouring DMRT3, the major gene for gait. We detected selection signatures encompassing several genes in the Baicha Iron Hoof horse that represent good biological candidates for hoof health, including the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes. In addition, an analysis of regional subgroups (Asian compared to European) identified a single locus on ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the DOM2 horse clade. Conclusions: Genomic variation at these loci in the Baicha Iron Hoof may be leveraged in other horse populations to identify animals with superior hoof health or those at risk of hoof-related pathologies. The overlap between the selection signature in Asian horses with the DOM2 selection peak raises questions about the nature of horse domestication events, which may have involved a prehistoric clade other than DOM2 that has not yet been identified.
© 2023. The Author(s).
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Publication Date: 2023-01-19 PubMed ID: 36658473PubMed Central: PMC9854188DOI: 10.1186/s12864-023-09116-8Google 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 explores the genetic modifications that thousands of years of natural and artificial selection have imposed on the Chinese Mongolian horse populations. By examining the genomic signatures of these horse populations, the study reveals clues about how humans have selectively bred horses for certain traits and how these animals have adapted to a variety of environments.

Research Methodology

  • The researchers utilized Genome-wide Single Nucleotide Polymorphisms (SNPs) from five distinctive Chinese Mongolian horse populations to identify beneficial alterations in their genome for specific population traits, including gait, black coat colour, and hoof quality.
  • Other horse breeds from across the globe were included for comparison, in a bid to identify signs of regional-specific genetic selection.

Key Findings

  • The researchers found a highly significant selection peak for a specific trait, gait, in the Wushen horse population. This peak was found in the region on Equestrian Chromosome 23 (ECA23) carrying the DMRT3 gene, which is considered the primary gene responsible for gait.
  • In the Baicha Iron Hoof horse, selection signatures were detected around multiple genes believed to be crucial for hoof health, namely CSPG4, PEAK1, EXPH5, WWP2, and HAS3.
  • Moreover, a comparison between Asian and European horse subgroups revealed a unique locus on ECA3 containing the ZFPM1 gene. This has been identified as a selection marker tied to a significant horse domestication event leading to the formation of the DOM2 horse clade.

Implications and Conclusions

  • The research concluded that these genetic variations discovered in the Baicha Iron Hoof horse could be utilized in other horse populations to identify those with superior hoof health or potential risks of hoof-related pathologies.
  • The study also touched on multiple questions surrounding horse domestication events, particularly the discovery of shared selection peaks between Asian horses and the DOM2 clade, suggesting other unidentified prehistoric horse clades may have played a role in horse domestication.

Cite This Article

APA
Han H, Randhawa IAS, MacHugh DE, McGivney BA, Katz LM, Dugarjaviin M, Hill EW. (2023). Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health. BMC Genomics, 24(1), 35. https://doi.org/10.1186/s12864-023-09116-8

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 24
Issue: 1
Pages: 35

Researcher Affiliations

Han, Haige
  • Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China.
Randhawa, Imtiaz A S
  • Animal Genetics Laboratory, School of Veterinary Science, University of Queensland, Brisbane, Australia.
MacHugh, David E
  • UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.
  • UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04V1W8, Ireland.
McGivney, Beatrice A
  • Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3, Ireland.
Katz, Lisa M
  • UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04V1W8, Ireland.
Dugarjaviin, Manglai
  • Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China.
Hill, Emmeline W
  • UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland. emmeline.hill@ucd.ie.
  • Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3, Ireland. emmeline.hill@ucd.ie.

MeSH Terms

  • Animals
  • Adaptor Proteins, Signal Transducing / genetics
  • Genome
  • Hoof and Claw
  • Horses / genetics
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Selection, Genetic
  • Ubiquitin-Protein Ligases / genetics
  • Adaptation, Biological / genetics

Grant Funding

  • 2021BS03040 / National Natural Science Foundation of Inner Mongolia
  • QN202127 / Youth Fund Project of College of Animal Science of Inner Mongolia Agricultural University
  • 11/PI/1166 / Science Foundation Ireland

Conflict of Interest Statement

We declare no conflict of interest.

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