Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array

Area of Science:

• Canine genomics
• Comparative genomics
• Genetic variation

Background:

• Copy number variants (CNVs) significantly contribute to phenotypic diversity and can cause diseases in various species, including dogs.
• Previous canine CNV studies relied on high-resolution comparative genomic hybridization arrays.
• This research presents the first CNV investigation in dogs utilizing the CanineHD 170K genotyping array.

Purpose of the Study:

• To evaluate the performance of the CanineHD array for CNV detection in dogs.
• To identify novel and breed-specific CNV regions in a large canine dataset.
• To expand the catalog of canine CNV regions and identify candidate genes associated with traits and diseases.

Main Methods:

• Analysis of the largest dataset to date for canine CNV discovery, comprising 351 dogs from 30 breeds.
• Application of stringent criteria for CNV identification using the CanineHD 170K genotyping array.
• Characterization of CNV regions, including overlap with annotated genes and identification of breed-specific variants.

Main Results:

• Identification of 72 CNV regions, with 38 overlapping 148 annotated genes.
• Discovery of 29 novel CNV regions encompassing 44 genes.
• Identification of 15 breed-specific CNV regions (14 novel), some overlapping with putative disease susceptibility genes. Human orthologs of 23 identified genes are known to be dosage-sensitive.

Conclusions:

• The CanineHD array is effective for detecting canine CNVs.
• The study significantly extends the catalog of canine CNV regions with numerous novel discoveries.
• These novel CNV regions and associated genes provide valuable resources for future research into canine phenotypic variation and disease susceptibility.