Copy number variation underlies complex phenotypes in domestic dog breeds and other canids

Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a compr...

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Autores: Serres-Armero, Aitor|||0000-0003-1679-811X, Davis, Brian W.|||0000-0002-6121-135X, Povolotskaya, Inna S.|||0000-0001-6621-232X, Morcillo-Suarez, Carlos, Plassais, Jocelyn|||0000-0002-2112-1595, Juan, David|||0000-0003-1912-9667, Ostrander, Elaine A.|||0000-0001-6075-9738, Marquès i Bonet, Tomàs|||0000-0002-5597-3075
Tipo de recurso: artículo
Fecha de publicación:2021
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:256109
Acceso en línea:https://ddd.uab.cat/record/256109
https://dx.doi.org/urn:doi:10.1101/gr.266049.120
Access Level:acceso abierto
Palabra clave:Genome assembly
Transcriptome assembly
Copy number variation
Rangifer tarandus
Genome annotation
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spelling Copy number variation underlies complex phenotypes in domestic dog breeds and other canidsSerres-Armero, Aitor|||0000-0003-1679-811XDavis, Brian W.|||0000-0002-6121-135XPovolotskaya, Inna S.|||0000-0001-6621-232XMorcillo-Suarez, CarlosPlassais, Jocelyn|||0000-0002-2112-1595Juan, David|||0000-0003-1912-9667Ostrander, Elaine A.|||0000-0001-6075-9738Marquès i Bonet, Tomàs|||0000-0002-5597-3075Genome assemblyTranscriptome assemblyCopy number variationRangifer tarandusGenome annotationExtreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds. 22021-01-0120212021-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/256109https://dx.doi.org/urn:doi:10.1101/gr.266049.120reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengEuropean Commission https://doi.org/10.13039/501100000780 864203Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 BFU2017-86471-PAgencia Estatal de Investigación https://doi.org/10.13039/501100011033 CEX2018-000792-MAgència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2017/SGR-880open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2561092026-06-06T12:50:31Z
dc.title.none.fl_str_mv Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
title Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
spellingShingle Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
Serres-Armero, Aitor|||0000-0003-1679-811X
Genome assembly
Transcriptome assembly
Copy number variation
Rangifer tarandus
Genome annotation
title_short Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
title_full Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
title_fullStr Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
title_full_unstemmed Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
title_sort Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
dc.creator.none.fl_str_mv Serres-Armero, Aitor|||0000-0003-1679-811X
Davis, Brian W.|||0000-0002-6121-135X
Povolotskaya, Inna S.|||0000-0001-6621-232X
Morcillo-Suarez, Carlos
Plassais, Jocelyn|||0000-0002-2112-1595
Juan, David|||0000-0003-1912-9667
Ostrander, Elaine A.|||0000-0001-6075-9738
Marquès i Bonet, Tomàs|||0000-0002-5597-3075
author Serres-Armero, Aitor|||0000-0003-1679-811X
author_facet Serres-Armero, Aitor|||0000-0003-1679-811X
Davis, Brian W.|||0000-0002-6121-135X
Povolotskaya, Inna S.|||0000-0001-6621-232X
Morcillo-Suarez, Carlos
Plassais, Jocelyn|||0000-0002-2112-1595
Juan, David|||0000-0003-1912-9667
Ostrander, Elaine A.|||0000-0001-6075-9738
Marquès i Bonet, Tomàs|||0000-0002-5597-3075
author_role author
author2 Davis, Brian W.|||0000-0002-6121-135X
Povolotskaya, Inna S.|||0000-0001-6621-232X
Morcillo-Suarez, Carlos
Plassais, Jocelyn|||0000-0002-2112-1595
Juan, David|||0000-0003-1912-9667
Ostrander, Elaine A.|||0000-0001-6075-9738
Marquès i Bonet, Tomàs|||0000-0002-5597-3075
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genome assembly
Transcriptome assembly
Copy number variation
Rangifer tarandus
Genome annotation
topic Genome assembly
Transcriptome assembly
Copy number variation
Rangifer tarandus
Genome annotation
description Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.
publishDate 2021
dc.date.none.fl_str_mv 2
2021-01-01
2021
2021-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/256109
https://dx.doi.org/urn:doi:10.1101/gr.266049.120
url https://ddd.uab.cat/record/256109
https://dx.doi.org/urn:doi:10.1101/gr.266049.120
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv European Commission https://doi.org/10.13039/501100000780 864203
Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 BFU2017-86471-P
Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 CEX2018-000792-M
Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2017/SGR-880
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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