A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
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-...
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ftdoajarticles:oai:doaj.org/article:b6a4488961924324a592eae5e3f4d3b4 2023-05-15T15:50:27+02:00 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 2011-08-01T00:00:00Z https://doi.org/10.1186/1471-2164-12-414 https://doaj.org/article/b6a4488961924324a592eae5e3f4d3b4 EN eng BMC http://www.biomedcentral.com/1471-2164/12/414 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-12-414 1471-2164 https://doaj.org/article/b6a4488961924324a592eae5e3f4d3b4 BMC Genomics, Vol 12, Iss 1, p 414 (2011) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2011 ftdoajarticles https://doi.org/10.1186/1471-2164-12-414 2022-12-31T09:15:25Z 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. Article in Journal/Newspaper Canis lupus gray wolf Directory of Open Access Journals: DOAJ Articles BMC Genomics 12 1 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
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Biotechnology TP248.13-248.65 Genetics QH426-470 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 |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
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. |
format |
Article in Journal/Newspaper |
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 |
title |
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_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_sort |
high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog |
publisher |
BMC |
publishDate |
2011 |
url |
https://doi.org/10.1186/1471-2164-12-414 https://doaj.org/article/b6a4488961924324a592eae5e3f4d3b4 |
genre |
Canis lupus gray wolf |
genre_facet |
Canis lupus gray wolf |
op_source |
BMC Genomics, Vol 12, Iss 1, p 414 (2011) |
op_relation |
http://www.biomedcentral.com/1471-2164/12/414 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-12-414 1471-2164 https://doaj.org/article/b6a4488961924324a592eae5e3f4d3b4 |
op_doi |
https://doi.org/10.1186/1471-2164-12-414 |
container_title |
BMC Genomics |
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12 |
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1 |
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1766385389614923776 |