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Home / Equine Research Bank / Front Vet Sci / Genome-wide copy number variation detection in a large cohor...
Frontiers in veterinary science2023; 10; 1296213; doi: 10.3389/fvets.2023.1296213

Genome-wide copy number variation detection in a large cohort of diverse horse breeds by whole-genome sequencing.

Abstract: Understanding how genetic variants alter phenotypes is an essential aspect of genetic research. Copy number variations (CNVs), a type of prevalent genetic variation in the genome, have been the subject of extensive study for decades. Numerous CNVs have been identified and linked to specific phenotypes and diseases in horses. However, few studies utilizing whole-genome sequencing to detect CNVs in large horse populations have been conducted. Here, we performed whole-genome sequencing on a large cohort of 97 horses from 16 horse populations using Illumina Hiseq panels to detect common and breed-specific CNV regions (CNVRs) genome-wide. This is the largest number of breeds and individuals utilized in a whole genome sequencing-based horse CNV study, employing racing, sport, local, primitive, draft, and pony breeds from around the world. We identified 5,053 to 44,681 breed CNVRs in each of the 16 horse breeds, with median lengths ranging from 1.9 kb to 8 kb. Furthermore, using statistics we analyzed the population differentiation of autosomal CNVRs in three diverse horse populations (Thoroughbred, Yakutian, and Przewalski's horse). Functional annotations were performed on CNVR-overlapping genes and revealed that population-differentiated candidate genes ( and ) may be involved in selection and adaptation. Our pilot study has provided the horse genetic research community with a large and valuable CNVR dataset and has identified many potential horse breeding targets that require further validation and in-depth investigation.
Copyright © 2023 Tang, Zhu, Ren, Chen, Li and Gu.
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Publication Date: 2023-11-22 PubMed ID: 38076560PubMed Central: PMC10710158DOI: 10.3389/fvets.2023.1296213Google 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 presents a study where genetic variations called copy number variations (CNVs) were detected in different breeds of horses using whole-genome sequencing. The study involved 97 horses from 16 different breeds and provided a comprehensive dataset for the horse genetic research community.

Introduction and Methodology

  • The research focused on Copy Number Variations (CNVs), a common type of genetic variation in the genome of living organisms. These are alterations of the DNA of a genome that result in the cell having an abnormal number of copies of one or more sections of the DNA. These variations are associated with certain characteristics or diseases in horses.
  • The researchers used Illumina Hiseq whole-genome sequencing panels for high throughput sequencing. This technique was applied to 97 horses from 16 different horse populations globally including racing, sport, local, primitive, draft, and pony breeds.
  • The goal was to find common and breed-specific CNV regions (CNVRs) across the genome. This is an area of the genome that is capable of having CNVs.

Results and Findings

  • The research identified between 5,053 to 44,681 breed-specific CNVRs in each of the 16 horse breeds, with the lengths of these CNVRs varying between 1.9 kb to 8 kb.
  • Population differentiation was also assessed in three diverse horse populations: Thoroughbred, Yakutian, and Przewalski’s horse.
  • Functional annotations were carried out on genes overlapping the identified CNVRs, meaning the researchers examined what these genes do and how they function with their related CNVs.
  • Two candidate genes, GTF2I and RP1, which may be involved in selection and adaptation, showed population differentiated status, hinting at potential breed-specific functional implications.

Conclusion and Future Directions

  • The researchers concluded that the pilot study has yielded a valuable dataset for the horse genetic research community. This extensive dataset of CNVRs can further aid in understanding the genetic variation and diversity among different horse breeds.
  • The study has also identified potential breeding targets for future research. However, these targets need further validation and in-depth analysis to fully understand their roles and implications.

Cite This Article

APA
Tang X, Zhu B, Ren R, Chen B, Li S, Gu J. (2023). Genome-wide copy number variation detection in a large cohort of diverse horse breeds by whole-genome sequencing. Front Vet Sci, 10, 1296213. https://doi.org/10.3389/fvets.2023.1296213

Publication

Frontiers in veterinary science
ISSN: 2297-1769
NlmUniqueID: 101666658
Country: Switzerland
Language: English
Volume: 10
Pages: 1296213
PII: 1296213

Researcher Affiliations

Tang, Xiangwei
  • College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
Zhu, Bo
  • Novogene Bioinformatics Institute, Beijing, China.
Ren, Ruimin
  • College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
Chen, Bin
  • College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
Li, Sheng
  • Maxun Biotechnology Institute, Changsha, China.
Gu, Jingjing
  • College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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