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

Schurink, Anouk; da Silva, Vinicius H.; Velie, Brandon D.; Dibbits, Bert W.; Crooijmans, Richard P.M.A.; Fran?ois, Liesbeth; Janssens, Steven; Stinckens, Anneleen; Blott, Sarah; Buys, Nadine; Lindgren, Gabriella; Ducro, Bart J.

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Authors

Anouk Schurink

Vinicius H. da Silva

Brandon D. Velie

Bert W. Dibbits

Richard P.M.A. Crooijmans

Liesbeth Fran?ois

Steven Janssens

Anneleen Stinckens

Nadine Buys

Gabriella Lindgren

Bart J. Ducro



Abstract

Background: 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.
Results: 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.
Conclusions: 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.

Citation

Schurink, A., da Silva, V. H., Velie, B. D., Dibbits, B. W., Crooijmans, R. P., Franҫois, L., …Ducro, B. J. (2018). Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genetics, 19, Article 49. https://doi.org/10.1186/s12863-018-0657-0

Journal Article Type Article
Acceptance Date Jul 19, 2018
Online Publication Date Jul 30, 2018
Publication Date Jul 30, 2018
Deposit Date Aug 1, 2018
Publicly Available Date Aug 1, 2018
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 19
Article Number 49
DOI https://doi.org/10.1186/s12863-018-0657-0
Keywords Copy number variations, Friesian horse, Genome-wide association study, Insect bite hypersensitivity
Public URL https://nottingham-repository.worktribe.com/output/895051
Publisher URL https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-018-0657-0
Contract Date Aug 1, 2018

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