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BMC genetics2018; 19(1); 49; doi: 10.1186/s12863-018-0657-0

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity.

Abstract: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.
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Publication Date: 2018-07-30 PubMed ID: 30060732PubMed Central: PMC6065148DOI: 10.1186/s12863-018-0657-0Google 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 copy number variations (CNVs) in Friesian horses, aiming to identify potential genetic risk factors for Insect Bite Hypersensitivity (IBH). The key findings suggest a clear link between the MHC region on ECA20 and IBH sensitivity in this horse breed, indicating that both single nucleotide polymorphisms (SNPs) and CNVs contribute to the disease’s complexity.

Study Objectives and Overview

  • The research focuses on understanding the role of structural genetic variations, particularly copy number variations (CNVs), in relation to diseases affecting horses’ welfare, specifically insect bite hypersensitivity (IBH).
  • The study aimed to identify CNVs and perform a genome-wide association (GWA) study on Friesian horses, a breed frequently affected by IBH.
  • IBH is a common seasonal allergy that causes skin inflammation in many horse breeds globally.

Methodology

  • The genotypes for the study were obtained using the Axiom® Equine Genotyping Array, which contains 670,796 SNPs, focusing on CNVs.
  • After performing a quality control of genotypes, 15,041 CNVs and 5,350 CNV regions (CNVRs) were identified in 222 Friesian horses.
  • The overall coverage of the total genome by CNVRs was 11.2%, with 49.2% of CNVRs containing genes, and 58% of CNVRs being novel.
  • A genome-wide association (GWA) analysis was performed, including both SNP and CNV based examination. About half of the sampled horses were affected by IBH.

Key Findings

  • The SNP-based analysis revealed a significant association between the MHC region on ECA20 and IBH in Friesian horses.
  • This association was also detected in the CNV-based analysis. However, the CNVs associated with IBH in Friesian horses were not often closely located to the SNPs identified as associated with IBH.
  • These results suggest a clear link between the MHC region on ECA20 and IBH sensitivity, implying that both SNPs and CNVs contribute to IBH sensitivity in Friesian horses.
  • This research adds to the knowledge of CNVs in horses and facilitates understanding of how the equine genome impacts phenotypic expression.

Implications

  • The study’s findings underline the complex genomic architecture of IBH, indicating it’s not just determined by single nucleotide differences, but also by more advanced structural variations such as CNVs.
  • The research reiterates the critical need for further analysis to verify these findings and to explore possible therapeutic interventions targeting these identified genetic risk factors for IBH.

Cite This Article

APA
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. (2018). Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genet, 19(1), 49. https://doi.org/10.1186/s12863-018-0657-0

Publication

BMC genetics
ISSN: 1471-2156
NlmUniqueID: 100966978
Country: England
Language: English
Volume: 19
Issue: 1
Pages: 49

Researcher Affiliations

Schurink, Anouk
  • Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands. anouk.schurink@wur.nl.
da Silva, Vinicius H
  • Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden.
  • Department of Animal Ecology, Netherlands Institute of Ecology, NIOO-KNAW, 6708, PB, Wageningen, the Netherlands.
Velie, Brandon D
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden.
Dibbits, Bert W
  • Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.
Crooijmans, Richard P M A
  • Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.
Franҫois, Liesbeth
  • KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium.
Janssens, Steven
  • KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium.
Stinckens, Anneleen
  • KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium.
Blott, Sarah
  • Reproductive Biology, Faculty of Medicine and Health Sciences, The University of Nottingham, Leicestershire, LE12 5RD, UK.
Buys, Nadine
  • KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium.
Lindgren, Gabriella
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden.
Ducro, Bart J
  • Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.

MeSH Terms

  • Animals
  • DNA Copy Number Variations
  • Genome-Wide Association Study / veterinary
  • Horses / genetics
  • Hypersensitivity / genetics
  • Hypersensitivity / veterinary
  • Insect Bites and Stings / genetics
  • Insect Bites and Stings / veterinary
  • Polymorphism, Single Nucleotide
  • Risk Factors

Conflict of Interest Statement

ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Hair samples from both cases and controls were collected with a written informed consent of the horse’s owner. It was considered that there was no need for an Animal Care and Ethics Committee approval according to the Dutch law after consultation with the Animal Experiment Expert from Wageningen University & Research. The Animal Welfare Officer thought it was not an animal experiment as referred to in the Dutch Act on Animal Experiments. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: Richard PMA Crooijmans is a Deputy Section Editor for BMC Genetics. As for the rest, there are no competing interests. PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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