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Home / Equine Research Bank / Mol Ecol Resour / Genetic variation and domestication of horses revealed by 10...
Molecular ecology resources2023; 23(7); 1656-1672; doi: 10.1111/1755-0998.13818

Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing.

Abstract: Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.
© 2023 John Wiley & Sons Ltd.
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Publication Date: 2023-05-31 PubMed ID: 37259205DOI: 10.1111/1755-0998.13818Google Scholar: Lookup
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  • Journal Article

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 the study of genetic variations in horses to improve breeding conservation and welfare, with particular emphasis on structural variants (SVs) and their influence on the genome-wide gene regulatory networks.

Objective of the Study

  • The primary objective of this research was to de novo assemble 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and to analyse horse SVs using a multi-assembly approach.
  • This would enable the researchers to gain deeper insights into the accumulated mammalian-wide interspersed repeats related to long interspersed nuclear elements, as they hypothesized it might be a horse-specific method to modulate genome-wide gene regulatory networks.

Key Findings of the Study

  • This research found evidence that olfactory receptors were frequently lost and had accumulated deleterious mutations. However, these mutations were not purged during horse domestication.
  • The study also examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were found to be significantly enriched by breed-specific SVs.
  • Examining the genomes, the researchers identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome.

Functional Implications of Findings

  • Several novel insertions might have potential functional consequences, as 519 were discovered to reside within 449 gene bodies.
  • These genes mainly involve in pathogen recognition, innate immune responses, and drug metabolism, which may provide an indication of breed-specific body function enhancements.

Finding Connections with Breed Characteristics

  • The study went further to analyze 97 horses with a comparative population genomics approach combining with public data, aiming to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study.

Conclusion and Implications

  • The study’s findings and the comprehensive genetic variation resource will help provide new scientific evidence for horse domestication, understanding of the genetic mechanism underlying the phenotypic evolution of horses and support further genetic studies of horses.

Cite This Article

APA
Gu J, Li S, Zhu B, Liang Q, Chen B, Tang X, Chen C, Wu DD, Li Y. (2023). Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing. Mol Ecol Resour, 23(7), 1656-1672. https://doi.org/10.1111/1755-0998.13818

Publication

Molecular ecology resources
ISSN: 1755-0998
NlmUniqueID: 101465604
Country: England
Language: English
Volume: 23
Issue: 7
Pages: 1656-1672

Researcher Affiliations

Gu, Jingjing
  • College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China.
Li, Sheng
  • Maxun Biotechnology Institute, Changsha, China.
Zhu, Bo
  • Novogene Bioinformatics Institute, Beijing, China.
Liang, Qiqi
  • Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.
Chen, Bin
  • College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China.
Tang, Xiangwei
  • College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China.
Chen, Chujie
  • College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China.
Wu, Dong-Dong
  • State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Li, Yan
  • State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, China.

MeSH Terms

  • Animals
  • Horses / genetics
  • Domestication
  • Genome / genetics
  • Sequence Analysis, DNA
  • Genetic Variation
  • Chromosomes
  • Mammals / genetics

Grant Funding

  • 31501000 / National Natural Science Foundation of China
  • 2019QZKK0501 / Second Tibetan Plateau Scientific Expedition and Research (STEP) Program
  • XDA2004010302 / The Strategic Priority Research Program of the Chinese Academy of Sciences
  • The Young Academic and Technical Leader Raising Foundation of Yunnan Province

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Citations

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