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

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Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. / Vaysse, Amaury; Ratnakumar, Abhirami; Derrien, Thomas; Axelsson, Erik; Pielberg, Gerli Rosengren; Sigurdsson, Snaevar; Fall, Tove; Seppälä, Eija H.; Hansen, Mark S.T.; Lawley, Cindy T.; Karlsson, Elinor K.; Bannasch, Danika; Vilà, Carles; Lohi, Hannes; Galibert, Francis; Fredholm, Merete; Häggström, Jens; Hedhammar, Åke; André, Catherine; Lindblad-Toh, Kerstin; Hitte, Christophe; Webster, Matthew T.

I: PLoS Genetics, Bind 7, Nr. 10, 2011.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Vaysse, A, Ratnakumar, A, Derrien, T, Axelsson, E, Pielberg, GR, Sigurdsson, S, Fall, T, Seppälä, EH, Hansen, MST, Lawley, CT, Karlsson, EK, Bannasch, D, Vilà, C, Lohi, H, Galibert, F, Fredholm, M, Häggström, J, Hedhammar, Å, André, C, Lindblad-Toh, K, Hitte, C & Webster, MT 2011, 'Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping' PLoS Genetics, bind 7, nr. 10. https://doi.org/10.1371/journal.pgen.1002316

APA

Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Pielberg, G. R., Sigurdsson, S., ... Webster, M. T. (2011). Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genetics, 7(10). https://doi.org/10.1371/journal.pgen.1002316

Vancouver

Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Pielberg GR, Sigurdsson S o.a. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genetics. 2011;7(10). https://doi.org/10.1371/journal.pgen.1002316

Author

Vaysse, Amaury ; Ratnakumar, Abhirami ; Derrien, Thomas ; Axelsson, Erik ; Pielberg, Gerli Rosengren ; Sigurdsson, Snaevar ; Fall, Tove ; Seppälä, Eija H. ; Hansen, Mark S.T. ; Lawley, Cindy T. ; Karlsson, Elinor K. ; Bannasch, Danika ; Vilà, Carles ; Lohi, Hannes ; Galibert, Francis ; Fredholm, Merete ; Häggström, Jens ; Hedhammar, Åke ; André, Catherine ; Lindblad-Toh, Kerstin ; Hitte, Christophe ; Webster, Matthew T. / Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. I: PLoS Genetics. 2011 ; Bind 7, Nr. 10.

Bibtex

@article{cacedd051942488db3766c2d1283cd23,
title = "Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping",
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.",
author = "Amaury Vaysse and Abhirami Ratnakumar and Thomas Derrien and Erik Axelsson and Pielberg, {Gerli Rosengren} and Snaevar Sigurdsson and Tove Fall and Sepp{\"a}l{\"a}, {Eija H.} and Hansen, {Mark S.T.} and Lawley, {Cindy T.} and Karlsson, {Elinor K.} and Danika Bannasch and Carles Vil{\`a} and Hannes Lohi and Francis Galibert and Merete Fredholm and Jens H{\"a}ggstr{\"o}m and {\AA}ke Hedhammar and Catherine Andr{\'e} and Kerstin Lindblad-Toh and Christophe Hitte and Webster, {Matthew T.}",
year = "2011",
doi = "10.1371/journal.pgen.1002316",
language = "English",
volume = "7",
journal = "P L o S Genetics",
issn = "1553-7390",
publisher = "Public Library of Science",
number = "10",

}

RIS

TY - JOUR

T1 - Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping

AU - Vaysse, Amaury

AU - Ratnakumar, Abhirami

AU - Derrien, Thomas

AU - Axelsson, Erik

AU - Pielberg, Gerli Rosengren

AU - Sigurdsson, Snaevar

AU - Fall, Tove

AU - Seppälä, Eija H.

AU - Hansen, Mark S.T.

AU - Lawley, Cindy T.

AU - Karlsson, Elinor K.

AU - Bannasch, Danika

AU - Vilà, Carles

AU - Lohi, Hannes

AU - Galibert, Francis

AU - Fredholm, Merete

AU - Häggström, Jens

AU - Hedhammar, Åke

AU - André, Catherine

AU - Lindblad-Toh, Kerstin

AU - Hitte, Christophe

AU - Webster, Matthew T.

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

U2 - 10.1371/journal.pgen.1002316

DO - 10.1371/journal.pgen.1002316

M3 - Journal article

VL - 7

JO - P L o S Genetics

JF - P L o S Genetics

SN - 1553-7390

IS - 10

ER -

ID: 35089577