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

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  • dc.contributor.author Serres Armero, Aitor, 1992-
  • dc.contributor.author Davis, Brian W.
  • dc.contributor.author Povolotskaya, Inna, 1986-
  • dc.contributor.author Morcillo Suárez, Carlos, 1969-
  • dc.contributor.author Plassais, Jocelyn
  • dc.contributor.author Juan, David
  • dc.contributor.author Ostrander, Elaine A.
  • dc.contributor.author Marquès i Bonet, Tomàs, 1975-
  • dc.date.accessioned 2021-05-10T07:38:58Z
  • dc.date.issued 2021
  • dc.description.abstract 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.
  • dc.description.sponsorship J.P. and E.A.O. were funded by the Intramural Program of the National Human Genome Research Institute of the National Institutes of Health. T.M.-B. was funded by European Research Council ERC-CON-2019-864203, BFU2017-86471-P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu,” funded by the Agencia Estatal de Investigación (CEX2018-000792-M), Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res. 2021;31(5):762-74. DOI: 10.1101/gr.266049.120
  • dc.identifier.doi http://dx.doi.org/10.1101/gr.266049.120
  • dc.identifier.issn 1088-9051
  • dc.identifier.uri http://hdl.handle.net/10230/47364
  • dc.language.iso eng
  • dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)
  • dc.relation.ispartof Genome Res. 2021;31(5):762-74
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
  • dc.rights © 2021 Serres-Armero et al.; Published by Cold Spring Harbor Laboratory Press. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
  • dc.title Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/acceptedVersion

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