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-...
Published in: | BMC Genomics |
---|---|
Main Authors: | , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Springer Science and Business Media LLC
2011
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1186/1471-2164-12-414 http://link.springer.com/content/pdf/10.1186/1471-2164-12-414.pdf http://link.springer.com/article/10.1186/1471-2164-12-414/fulltext.html https://link.springer.com/content/pdf/10.1186/1471-2164-12-414.pdf |
id |
crspringernat:10.1186/1471-2164-12-414 |
---|---|
record_format |
openpolar |
spelling |
crspringernat:10.1186/1471-2164-12-414 2023-05-15T15:50:29+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 http://dx.doi.org/10.1186/1471-2164-12-414 http://link.springer.com/content/pdf/10.1186/1471-2164-12-414.pdf http://link.springer.com/article/10.1186/1471-2164-12-414/fulltext.html https://link.springer.com/content/pdf/10.1186/1471-2164-12-414.pdf en eng Springer Science and Business Media LLC http://www.springer.com/tdm BMC Genomics volume 12, issue 1 ISSN 1471-2164 Genetics Biotechnology journal-article 2011 crspringernat https://doi.org/10.1186/1471-2164-12-414 2022-01-04T08:25:29Z 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 Springer Nature (via Crossref) BMC Genomics 12 1 |
institution |
Open Polar |
collection |
Springer Nature (via Crossref) |
op_collection_id |
crspringernat |
language |
English |
topic |
Genetics Biotechnology |
spellingShingle |
Genetics Biotechnology 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 |
Genetics Biotechnology |
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 |
Springer Science and Business Media LLC |
publishDate |
2011 |
url |
http://dx.doi.org/10.1186/1471-2164-12-414 http://link.springer.com/content/pdf/10.1186/1471-2164-12-414.pdf http://link.springer.com/article/10.1186/1471-2164-12-414/fulltext.html https://link.springer.com/content/pdf/10.1186/1471-2164-12-414.pdf |
genre |
Canis lupus gray wolf |
genre_facet |
Canis lupus gray wolf |
op_source |
BMC Genomics volume 12, issue 1 ISSN 1471-2164 |
op_rights |
http://www.springer.com/tdm |
op_doi |
https://doi.org/10.1186/1471-2164-12-414 |
container_title |
BMC Genomics |
container_volume |
12 |
container_issue |
1 |
_version_ |
1766385433087836160 |