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Home / Equine Research Bank / Anim Genet / Detection of copy number variants in the horse genome and ex...
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.
            1. Kim YM, Ha SJ, Seong HS, Choi JY, Baek HJ, Yang BC, Choi JW, Kim NY. Identification of Copy Number Variations in Four Horse Breed Populations in South Korea. Animals (Basel) 2022 Dec 12;12(24).
              doi: 10.3390/ani12243501pubmed: 36552421google scholar: lookup
            2. Laseca N, Molina A, Valera M, Antonini A, Demyda-Peyrás S. Copy Number Variation (CNV): A New Genomic Insight in Horses. Animals (Basel) 2022 Jun 2;12(11).
              doi: 10.3390/ani12111435pubmed: 35681904google scholar: lookup
            3. Wang M, Liu Y, Bi X, Ma H, Zeng G, Guo J, Guo M, Ling Y, Zhao C. Genome-Wide Detection of Copy Number Variants in Chinese Indigenous Horse Breeds and Verification of CNV-Overlapped Genes Related to Heat Adaptation of the Jinjiang Horse. Genes (Basel) 2022 Mar 28;13(4).
              doi: 10.3390/genes13040603pubmed: 35456409google scholar: lookup
            4. Fernandes AC, da Silva VH, Goes CP, Moreira GCM, Godoy TF, Ibelli AMG, Peixoto JO, Cantão ME, Ledur MC, de Rezende FM, Coutinho LL. Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics 2021 May 17;22(1):354.
              doi: 10.1186/s12864-021-07676-1pubmed: 34001004google scholar: lookup
            5. Ghosh S, Davis BW, Rosengren M, Jevit MJ, Castaneda C, Arnold C, Jaxheimer J, Love CC, Varner DD, Lindgren G, Wade CM, Raudsepp T. Characterization of A Homozygous Deletion of Steroid Hormone Biosynthesis Genes in Horse Chromosome 29 as A Risk Factor for Disorders of Sex Development and Reproduction. Genes (Basel) 2020 Feb 27;11(3).
              doi: 10.3390/genes11030251pubmed: 32120906google scholar: lookup
            6. Solé M, Ablondi M, Binzer-Panchal A, Velie BD, Hollfelder N, Buys N, Ducro BJ, François L, Janssens S, Schurink A, Viklund Å, Eriksson S, Isaksson A, Kultima H, Mikko S, Lindgren G. Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics 2019 Oct 22;20(1):759.
              doi: 10.1186/s12864-019-6141-zpubmed: 31640551google scholar: lookup
            7. Velie BD, Fegraeus KJ, Solé M, Rosengren MK, Røed KH, Ihler CF, Strand E, Lindgren G. A genome-wide association study for harness racing success in the Norwegian-Swedish coldblooded trotter reveals genes for learning and energy metabolism. BMC Genet 2018 Aug 29;19(1):80.
              doi: 10.1186/s12863-018-0670-3pubmed: 30157760google scholar: lookup
            8. Schurink A, da Silva VH, Velie BD, Dibbits BW, Crooijmans RPMA, Franҫois L, Janssens S, Stinckens A, Blott S, Buys N, Lindgren G, Ducro BJ. Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genet 2018 Jul 30;19(1):49.
              doi: 10.1186/s12863-018-0657-0pubmed: 30060732google scholar: lookup
            9. Draper ACE, Piercy RJ. Pathological classification of equine recurrent laryngeal neuropathy. J Vet Intern Med 2018 Jul;32(4):1397-1409.
              doi: 10.1111/jvim.15142pubmed: 29691904google scholar: lookup
            10. Todd ET, Ho SYW, Thomson PC, Ang RA, Velie BD, Hamilton NA. Founder-specific inbreeding depression affects racing performance in Thoroughbred horses. Sci Rep 2018 Apr 18;8(1):6167.
              doi: 10.1038/s41598-018-24663-xpubmed: 29670190google scholar: lookup
            11. Walker LC, Wiggins GA, Pearson JF. The Role of Constitutional Copy Number Variants in Breast Cancer. Microarrays (Basel) 2015 Sep 8;4(3):407-23.
              doi: 10.3390/microarrays4030407pubmed: 27600231google scholar: lookup
            12. McQueen CM, Dindot SV, Foster MJ, Cohen ND. Genetic Susceptibility to Rhodococcus equi. J Vet Intern Med 2015 Nov-Dec;29(6):1648-59.
              doi: 10.1111/jvim.13616pubmed: 26340305google scholar: lookup
            13. Ghosh S, Qu Z, Das PJ, Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear TL, Adelson DL, Chowdhary BP, Raudsepp T. Copy number variation in the horse genome. PLoS Genet 2014 Oct;10(10):e1004712.
              doi: 10.1371/journal.pgen.1004712pubmed: 25340504google scholar: lookup
            14. McQueen CM, Doan R, Dindot SV, Bourquin JR, Zlatev ZZ, Chaffin MK, Blodgett GP, Ivanov I, Cohen ND. Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PLoS One 2014;9(6):e98710.
              doi: 10.1371/journal.pone.0098710pubmed: 24892408google scholar: lookup
            15. Zhao Q, Han MJ, Sun W, Zhang Z. Copy number variations among silkworms. BMC Genomics 2014 Mar 31;15:251.
              doi: 10.1186/1471-2164-15-251pubmed: 24684762google scholar: lookup
            16. Gurgul A, Semik E, Pawlina K, Szmatoła T, Jasielczuk I, Bugno-Poniewierska M. The application of genome-wide SNP genotyping methods in studies on livestock genomes. J Appl Genet 2014 May;55(2):197-208.
              doi: 10.1007/s13353-014-0202-4pubmed: 24566962google scholar: lookup
            17. Wang W, Wang S, Hou C, Xing Y, Cao J, Wu K, Liu C, Zhang D, Zhang L, Zhang Y, Zhou H. Genome-wide detection of copy number variations among diverse horse breeds by array CGH. PLoS One 2014;9(1):e86860.
              doi: 10.1371/journal.pone.0086860pubmed: 24497987google scholar: lookup
            18. Metzger J, Philipp U, Lopes MS, da Camara Machado A, Felicetti M, Silvestrelli M, Distl O. Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics 2013 Jul 18;14:487.
              doi: 10.1186/1471-2164-14-487pubmed: 23865711google scholar: lookup
            19. Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D. Whole-Genome Resequencing Analysis of Copy Number Variations Associated with Athletic Performance in Grassland-Thoroughbred. Animals (Basel) 2025 May 18;15(10).
              doi: 10.3390/ani15101458pubmed: 40427335google scholar: lookup
            20. Sharma NK, Singh P, Saha B, Bhardwaj A, Iquebal MA, Pal Y, Nayan V, Jaiswal S, Giri SK, Legha RA, Bhattacharya TK, Kumar D, Rai A. Genome wide landscaping of copy number variations for horse inter-breed variability. Anim Biotechnol 2025 Dec;36(1):2446251.
              doi: 10.1080/10495398.2024.2446251pubmed: 39791493google scholar: lookup
            21. Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X, Chai W, Khan MZ, Wang C. Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits. Front Vet Sci 2023;10:1334434.
              doi: 10.3389/fvets.2023.1334434pubmed: 38274664google scholar: lookup
            22. Tang X, Zhu B, Ren R, Chen B, Li S, Gu J. Genome-wide copy number variation detection in a large cohort of diverse horse breeds by whole-genome sequencing. Front Vet Sci 2023;10:1296213.
              doi: 10.3389/fvets.2023.1296213pubmed: 38076560google scholar: lookup
            23. Choudhury MP, Wang Z, Zhu M, Teng S, Yan J, Cao S, Yi G, Liu Y, Liao Y, Tang Z. Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses. Genes (Basel) 2023 Oct 13;14(10).
              doi: 10.3390/genes14101934pubmed: 37895283google scholar: lookup
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