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Home / Equine Research Bank / PLoS One / Genome-wide detection of copy number variations among divers...
PloS one2014; 9(1); e86860; doi: 10.1371/journal.pone.0086860

Genome-wide detection of copy number variations among diverse horse breeds by array CGH.

Abstract: Recent studies have found that copy number variations (CNVs) are widespread in human and animal genomes. CNVs are a significant source of genetic variation, and have been shown to be associated with phenotypic diversity. However, the effect of CNVs on genetic variation in horses is not well understood. In the present study, CNVs in 6 different breeds of mare horses, Mongolia horse, Abaga horse, Hequ horse and Kazakh horse (all plateau breeds) and Debao pony and Thoroughbred, were determined using aCGH. In total, seven hundred CNVs were identified ranging in size from 6.1 Kb to 0.57 Mb across all autosomes, with an average size of 43.08 Kb and a median size of 15.11 Kb. By merging overlapping CNVs, we found a total of three hundred and fifty-three CNV regions (CNVRs). The length of the CNVRs ranged from 6.1 Kb to 1.45 Mb with average and median sizes of 38.49 Kb and 13.1 Kb. Collectively, 13.59 Mb of copy number variation was identified among the horses investigated and accounted for approximately 0.61% of the horse genome sequence. Five hundred and eighteen annotated genes were affected by CNVs, which corresponded to about 2.26% of all horse genes. Through the gene ontology (GO), genetic pathway analysis and comparison of CNV genes among different breeds, we found evidence that CNVs involving 7 genes may be related to the adaptation to severe environment of these plateau horses. This study is the first report of copy number variations in Chinese horses, which indicates that CNVs are ubiquitous in the horse genome and influence many biological processes of the horse. These results will be helpful not only in mapping the horse whole-genome CNVs, but also to further research for the adaption to the high altitude severe environment for plateau horses.
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Publication Date: 2014-01-30 PubMed ID: 24497987PubMed Central: PMC3907382DOI: 10.1371/journal.pone.0086860Google 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 investigates the genetic variation in different breeds of horses, focusing on copy number variations (CNVs) which have been identified to affect a significant amount of biological processes. Through studying six different horse breeds, 700 CNVs were discovered, and the findings suggest CNVs may play a part in the adaptation process to harsh environments in plateau horses.

Method of Investigation and Findings

  • The research utilizes array CGH (Comparative Genomic Hybridization) to determine CNVs in six different mare horse breeds: Mongolia, Abaga, Hequ, and Kazakh horses (all plateau breeds), and Debao pony and Thoroughbred.
  • From this, 700 CNVs were detected, with sizes ranging between 6.1 Kb (kilobases) to 0.57 Mb (megabases) across all autosomes. The average size was calculated to be 43.08 Kb and a median size of 15.11 Kb.
  • By merging overlapping CNVs, three hundred and fifty-three CNV regions (CNVRs) were identified.
  • The whole CNVRs’ length fluctuated between 6.1 Kb to 1.45 Mb, with average and median sizes of 38.49 Kb and 13.1 Kb respectively.
  • The total area of copy number variation detected was approximately 13.59 Mb, accounting for about 0.61% of the entire horse genome sequence.

Affected Genes and Biological Implications

  • Five hundred and eighteen annotated genes were concluded to be affected by the CNVs, comprising around 2.26% of all horse genes.
  • Through the use of gene ontology (GO), genetic pathway analysis, and comparison of CNV genes among the different horse breeds, the study posits that 7 genes affected by CNVs might be related to how these plateau horses adapt to their severe environment.
  • Therefore, CNVs are theorized to greatly influence many biological processes in horses.

Contributions and Future Implications

  • This study is recognized as the first report of CNVs in Chinese horses, establishing that CNVs are widespread in the horse genome.
  • These findings provide a solid basis to not only map the whole-genome CNVs in horses, but also to conduct further studies on how plateau horses adapt to high altitude, harsh environments.

Cite This Article

APA
Wang W, Wang S, Hou C, Xing Y, Cao J, Wu K, Liu C, Zhang D, Zhang L, Zhang Y, Zhou H. (2014). Genome-wide detection of copy number variations among diverse horse breeds by array CGH. PLoS One, 9(1), e86860. https://doi.org/10.1371/journal.pone.0086860

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 9
Issue: 1
Pages: e86860
PII: e86860

Researcher Affiliations

Wang, Wei
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Wang, Shenyuan
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Hou, Chenglin
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Xing, Yanping
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Cao, Junwei
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Wu, Kaifeng
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Liu, Chunxia
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Zhang, Dong
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Zhang, Li
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Zhang, Yanru
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.
Zhou, Huanmin
  • College of Life Sciences Inner Mongolia Agricultural University, Hohhot, China ; Key Laboratory of Biological Manufacturing, Hohhot, China.

MeSH Terms

  • Adaptation, Physiological / genetics
  • Altitude
  • Animals
  • Chromosomes, Mammalian
  • Comparative Genomic Hybridization
  • DNA Copy Number Variations
  • Female
  • Gene Ontology
  • Genome
  • Horses / genetics

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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