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

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 t...

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Autores principales: Nicholas, Thomas J, Baker, Carl, Eichler, Evan E, Akey, Joshua M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166287/
https://www.ncbi.nlm.nih.gov/pubmed/21846351
http://dx.doi.org/10.1186/1471-2164-12-414
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author Nicholas, Thomas J
Baker, Carl
Eichler, Evan E
Akey, Joshua M
author_facet Nicholas, Thomas J
Baker, Carl
Eichler, Evan E
Akey, Joshua M
author_sort Nicholas, Thomas J
collection PubMed
description 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.
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spelling pubmed-31662872011-09-03 A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog Nicholas, Thomas J Baker, Carl Eichler, Evan E Akey, Joshua M BMC Genomics Research Article 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. BioMed Central 2011-08-16 /pmc/articles/PMC3166287/ /pubmed/21846351 http://dx.doi.org/10.1186/1471-2164-12-414 Text en Copyright ©2011 Nicholas et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Nicholas, Thomas J
Baker, Carl
Eichler, Evan E
Akey, Joshua M
A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
title A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
title_full A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
title_fullStr A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
title_full_unstemmed A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
title_short A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
title_sort high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166287/
https://www.ncbi.nlm.nih.gov/pubmed/21846351
http://dx.doi.org/10.1186/1471-2164-12-414
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