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

Author:

Serres-Armero AitorORCID,Davis Brian W.ORCID,Povolotskaya Inna S.ORCID,Morcillo-Suarez Carlos,Plassais JocelynORCID,Juan DavidORCID,Ostrander Elaine A.ORCID,Marques-Bonet TomasORCID

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.

Funder

National Human Genome Research Institute

National Institutes of Health

European Research Council

MINECO/FEDER

Howard Hughes International Early Career

Obra Social “La Caixa”

Secretaria d'Universitats i Recerca

CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya

Publisher

Cold Spring Harbor Laboratory

Subject

Genetics (clinical),Genetics

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