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Open Access Research article

A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog

Thomas J Nicholas1, Carl Baker1, Evan E Eichler12 and Joshua M Akey1*

Author Affiliations

1 Department of Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA. 98195, USA

2 Howard Hughes Medical Institute, Seattle, WA, USA

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BMC Genomics 2011, 12:414  doi:10.1186/1471-2164-12-414

Published: 16 August 2011

Abstract

Background

Structural variation contributes to the rich genetic and phenotypic diversity of the modern domestic dog, Canis lupus familiaris, although compared to other organisms, catalogs of canine copy number variants (CNVs) are poorly defined. To this end, we developed a customized high-density tiling array across the canine genome and used it to discover CNVs in nine genetically diverse dogs and a gray wolf.

Results

In total, we identified 403 CNVs that overlap 401 genes, which are enriched for defense/immunity, oxidoreductase, protease, receptor, signaling molecule and transporter genes. Furthermore, we performed detailed comparisons between CNVs located within versus outside of segmental duplications (SDs) and find that CNVs in SDs are enriched for gene content and complexity. Finally, we compiled all known dog CNV regions and genotyped them with a custom aCGH chip in 61 dogs from 12 diverse breeds. These data allowed us to perform the first population genetics analysis of canine structural variation and identify CNVs that potentially contribute to breed specific traits.

Conclusions

Our comprehensive analysis of canine CNVs will be an important resource in genetically dissecting canine phenotypic and behavioral variation.