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

Autor: Sarah C. Blott, Liesbeth Franҫois, Anneleen Stinckens, Brandon D. Velie, A. Schurink, Vinicius Henrique da Silva, Richard P. M. A. Crooijmans, Steven Janssens, Gabriella Lindgren, Nadine Buys, Bert Dibbits, Bart J. Ducro
Přispěvatelé: Animal Ecology (AnE)
Rok vydání: 2017
Předmět:
0301 basic medicine
ICELANDIC HORSES
Genome-wide association study
VARIANTS
Friesian horse
Risk Factors
Copy-number variation
Genetics (clinical)
POPULATION
2. Zero hunger
Genetics
Genetics & Heredity
education.field_of_study
biology
Copy number variations
Friesian horse
Genome-wide association study
Insect bite hypersensitivity
04 agricultural and veterinary sciences
international
Life Sciences & Biomedicine
Animal Breeding & Genomics
Research Article
CHROMOSOME 16P11.2
lcsh:QH426-470
DNA Copy Number Variations
biology.animal_breed
Population
Single-nucleotide polymorphism
Animal Breeding and Genomics
SUMMER ECZEMA
Polymorphism
Single Nucleotide
03 medical and health sciences
Hypersensitivity
SNP
Bio/Medical/Health - Genetics & Systems Biology
Animals
Fokkerij en Genomica
Genetic variability
Horses
Copy number variations
Fokkerij & Genomica
GENOME-WIDE ASSOCIATION
education
Genotyping
Science & Technology
IDENTIFICATION
0402 animal and dairy science
Insect Bites and Stings
040201 dairy & animal science
MAJOR HISTOCOMPATIBILITY COMPLEX
lcsh:Genetics
030104 developmental biology
RESOLUTION
WIAS
Insect bite hypersensitivity
Genome wide association study
MHC
Zdroj: BMC Genetics
BMC Genetics, Vol 19, Iss 1, Pp 1-13 (2018)
BMC Genetics, 19(1)
BMC Genetics 19 (2018) 1
BMC Genetics, 19:49. BioMed Central
ISSN: 1471-2156
Popis: 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. Electronic supplementary material The online version of this article (10.1186/s12863-018-0657-0) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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