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Animal genetics2012; 44(2); 206-208; doi: 10.1111/j.1365-2052.2012.02373.x

Detection of copy number variants in the horse genome and examination of their association with recurrent laryngeal neuropathy.

Abstract: We used the data from a recently performed genome-wide association study using the Illumina Equine SNP50 beadchip for the detection of copy number variants (CNVs) and examined their association with recurrent laryngeal neuropathy (RLN), an important equine upper airway disease compromising performance. A total of 2797 CNVs were detected for 477 horses, covering 229 kb and seven SNPs on average. Overlapping CNVs were merged to define 478 CNV regions (CNVRs). CNVRs, particularly deletions, were shown to be significantly depleted in genes. Fifty-two of the 67 common CNVRs (frequency ≥ 1%) were validated by association mapping, Mendelian inheritance, and/or Mendelian inconsistencies. None of the 67 common CNVRs were significantly associated with RLN when accounting for multiple testing. However, a duplication on chromosome 10 was detected in 10 cases (representing three breeds) and two unphenotyped parents but in none of the controls. The duplication was embedded in an 8-Mb haplotype shared across breeds.
© 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.
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Publication Date: 2012-05-14 PubMed ID: 22582820DOI: 10.1111/j.1365-2052.2012.02373.xGoogle Scholar: Lookup
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Summary

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The article discusses how researchers used a genome-wide association study to detect copy number variants (CNVs) in the horse genome, and their association with recurrent laryngeal neuropathy (RLN), an equine upper airway disease affecting performance. While none of the common CNVs were significantly linked with RLN, a duplication on chromosome 10 was detected in a few cases.

Methods of Research

  • The researchers used data from a genome-wide association study, using the Illumina Equine SNP50 beadchip. This technology allowed them to examine genetic variations across horse genomes to identify CNVs. CNVs are alterations in the DNA of an organism, where sections of the genome are repeated or duplicated. This can affect the function of genes and the organism’s overall health.
  • Through the genomic data, the researchers detected 2797 CNVs in 477 horses, covering an average of 229 Kb and seven SNPs (Single Nucleotide Polymorphisms, a type of genetic variation).
  • These overlapping CNVs were merged to define 478 CNV regions (CNVRs). Among these 478 CNVRs, deletions were found to be significantly depleted in genes.

Results

  • Out of 67 common CNVRs (those with a frequency of 1% or higher), 52 were validated by association mapping, Mendelian inheritance, and/or investigating inconsistencies in Mendelian inheritance.
  • No significant association was found between RLN and the common CNVRs when accounting for multiple testing procedures. This is important as it helps to reduce false-positive results. Thus, the researchers concluded that the common CNVRs do not play a significant role in the development of RLN.
  • However, a duplication was detected on chromosome 10 in 10 RLN-affected cases, spanning three different horse breeds. This duplication was also identified in two parents with no phenotypic symptoms but was absent in all the controls (healthy horses without RLN), indicating a potential correlation with the disease.
  • This chromosome 10 duplication was embedded in an 8-Mb haplotype, a group of genes that inherit together from a single parent, shared across different horse breeds. The cross-breed existence of this haplotype might suggest a common genetic foundation for RLN across different horse breeds.

Conclusion

  • The research provided valuable insights into the CNVs present within the horse genome. Although no immediate and clear association was found between common CNVRs and RLN, the detected uniqueness of some CNVRs, specifically a particular duplication on chromosome 10 in RLN-affected horses, may form the basis for further research in identifying genetic markers for RLN in horses.

Cite This Article

APA
Dupuis MC, Zhang Z, Durkin K, Charlier C, Lekeux P, Georges M. (2012). Detection of copy number variants in the horse genome and examination of their association with recurrent laryngeal neuropathy. Anim Genet, 44(2), 206-208. https://doi.org/10.1111/j.1365-2052.2012.02373.x

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 44
Issue: 2
Pages: 206-208

Researcher Affiliations

Dupuis, M C
  • Unit of Animal Genetics, GIGA-Research, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
Zhang, Z
    Durkin, K
      Charlier, C
        Lekeux, P
          Georges, M

            MeSH Terms

            • Animals
            • DNA Copy Number Variations / genetics
            • Genome / genetics
            • Genome-Wide Association Study
            • Haplotypes / genetics
            • Horse Diseases / genetics
            • Horses
            • Laryngeal Diseases / genetics
            • Laryngeal Diseases / pathology
            • Recurrent Laryngeal Nerve / pathology
            • Vagus Nerve Diseases / genetics

            Citations

            This article has been cited 23 times.
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