Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
Serres-Armero, Aitor (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Davis, Brian W. (Texas A&M University. Department of Veterinary Integrative Biosciences)
Povolotskaya, Inna S. (Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University)
Morcillo-Suarez, Carlos (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Plassais, Jocelyn (National Institutes of Health. Cancer Genetics and Comparative Genomics Branch)
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Ostrander, Elaine A. (National Institutes of Health. Cancer Genetics and Comparative Genomics Branch)
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)

Data:	2021
Resum:	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.
Ajuts:	European Commission 864203 Agencia Estatal de Investigación BFU2017-86471-P Agencia Estatal de Investigación CEX2018-000792-M Agència de Gestió d'Ajuts Universitaris i de Recerca 2017/SGR-880
Drets:	Aquest 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.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Genome assembly ; Transcriptome assembly ; Copy number variation ; Rangifer tarandus ; Genome annotation
Publicat a:	Genome research, Vol. 31 (May 2021) , p. 762-774, ISSN 1549-5469

DOI: 10.1101/gr.266049.120
PMID: 33863806

13 p, 3.0 MB

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