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Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping

Vaysse, A. and Ratnakumar, A. and Derrien, T. and Axelsson, Erik and Rosengren Pielberg, Gerli and Sigurdsson, Snaevar and Fall, T and Seppälä, E.H. and Hansen, M.S. and Lawley, Cindy T. and Karlsson, Elinor and Vilà, Carles and Bannasch, Danika and Lohi, Hannes and Galibert, Francis and Fredholm, M. and Häggström, Jens and Hedhammar, Åke and André, Catherine and Lindblad-Toh, Kerstin and Hitte, Christophe and Webster, M.T. (2011). Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS genetics. 7:10, 1-21
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Official URL: http://dx.doi.org/10.1371/journal.pgen.1002316

Abstract

The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.

Authors/Creators:Vaysse, A. and Ratnakumar, A. and Derrien, T. and Axelsson, Erik and Rosengren Pielberg, Gerli and Sigurdsson, Snaevar and Fall, T and Seppälä, E.H. and Hansen, M.S. and Lawley, Cindy T. and Karlsson, Elinor and Vilà, Carles and Bannasch, Danika and Lohi, Hannes and Galibert, Francis and Fredholm, M. and Häggström, Jens and Hedhammar, Åke and André, Catherine and Lindblad-Toh, Kerstin and Hitte, Christophe and Webster, M.T.
Title:Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping
Series/Journal:PLoS genetics (1553-7404)
Year of publishing :2011
Volume:7
Number:10
Page range:1-21
Number of Pages:18
Publisher:Public Library of Science
Associated Programs and Other Stakeholders:SLU - Research Areas for the Future > Future Animal Health and Welfare
ISSN:1553-7404
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Agris subject categories.:L Animal production > L10 Animal genetics and breeding
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 402 Animal and Dairy Science
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science
Agrovoc terms:Phenotypes, Dogs, Selection
Keywords:Phenotypic Variation, Dogs, Selection Mapping
URN:NBN:urn:nbn:se:slu:epsilon-e-1753
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-1753
Additional ID:
Type of IDID
Web of Science (WoS)000296665400017
DOI10.1371/journal.pgen.1002316
ID Code:10784
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Clinical Sciences
Deposited By: SLUpub Connector
Deposited On:14 Jan 2014 14:41
Metadata Last Modified:02 Dec 2014 11:03

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