Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.
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 breed...
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2011-10-01
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doaj-d1a5788aface4f22b8302a117fd494792020-11-24T21:41:58ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042011-10-01710e100231610.1371/journal.pgen.1002316Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.Amaury VaysseAbhirami RatnakumarThomas DerrienErik AxelssonGerli Rosengren PielbergSnaevar SigurdssonTove FallEija H SeppäläMark S T HansenCindy T LawleyElinor K KarlssonLUPA ConsortiumDanika BannaschCarles VilàHannes LohiFrancis GalibertMerete FredholmJens HäggströmAke HedhammarCatherine AndréKerstin Lindblad-TohChristophe HitteMatthew T WebsterThe 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.http://europepmc.org/articles/PMC3192833?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Amaury Vaysse Abhirami Ratnakumar Thomas Derrien Erik Axelsson Gerli Rosengren Pielberg Snaevar Sigurdsson Tove Fall Eija H Seppälä Mark S T Hansen Cindy T Lawley Elinor K Karlsson LUPA Consortium Danika Bannasch Carles Vilà Hannes Lohi Francis Galibert Merete Fredholm Jens Häggström Ake Hedhammar Catherine André Kerstin Lindblad-Toh Christophe Hitte Matthew T Webster |
spellingShingle |
Amaury Vaysse Abhirami Ratnakumar Thomas Derrien Erik Axelsson Gerli Rosengren Pielberg Snaevar Sigurdsson Tove Fall Eija H Seppälä Mark S T Hansen Cindy T Lawley Elinor K Karlsson LUPA Consortium Danika Bannasch Carles Vilà Hannes Lohi Francis Galibert Merete Fredholm Jens Häggström Ake Hedhammar Catherine André Kerstin Lindblad-Toh Christophe Hitte Matthew T Webster Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genetics |
author_facet |
Amaury Vaysse Abhirami Ratnakumar Thomas Derrien Erik Axelsson Gerli Rosengren Pielberg Snaevar Sigurdsson Tove Fall Eija H Seppälä Mark S T Hansen Cindy T Lawley Elinor K Karlsson LUPA Consortium Danika Bannasch Carles Vilà Hannes Lohi Francis Galibert Merete Fredholm Jens Häggström Ake Hedhammar Catherine André Kerstin Lindblad-Toh Christophe Hitte Matthew T Webster |
author_sort |
Amaury Vaysse |
title |
Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. |
title_short |
Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. |
title_full |
Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. |
title_fullStr |
Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. |
title_full_unstemmed |
Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. |
title_sort |
identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Genetics |
issn |
1553-7390 1553-7404 |
publishDate |
2011-10-01 |
description |
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. |
url |
http://europepmc.org/articles/PMC3192833?pdf=render |
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