Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

Luke Evans; Gancho Slavov; Eli Rodgers-Melnick; Joel Martin; Priya Ranjan; Wellington Muchero; Amy M Brunner; Wendy Schackwitz; Lee E. Gunter; Jin-Gui Chen; Gerald A. Tuskan; Stephen P. DiFazio

doi:10.1038/ng.3075

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

Luke Evans, Gancho Slavov, Eli Rodgers-Melnick, Joel Martin, Priya Ranjan, Wellington Muchero, Amy M Brunner, Wendy Schackwitz, Lee E. Gunter, Jin-Gui Chen, Gerald A. Tuskan, Stephen P. DiFazio

Adran y Gwyddorau Bywyd

Allbwn ymchwil: Cyfraniad at gyfnodolyn › Erthygl › adolygiad gan gymheiriaid

250 Dyfyniadau (Scopus)

738 Wedi eu Llwytho i Lawr (Pure)

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Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation.

Iaith wreiddiol	Saesneg
Tudalennau (o-i)	1089-1096
Nifer y tudalennau	8
Cyfnodolyn	Nature Genetics
Cyfrol	46
Rhif cyhoeddi	10
Dyddiad ar-lein cynnar	24 Awst 2014
Dynodwyr Gwrthrych Digidol (DOIs)	https://doi.org/10.1038/ng.3075
Statws	Cyhoeddwyd - 26 Medi 2014

NDC y CU

Mae’r allbwn hwn yn cyfrannu at y Nod(au) Datblygu Cynaliadwy canlynol

Mynediad at Ddogfen

10.1038/ng.3075

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associationsLlawysgrif awdur wedi’i dderbyn, 1.97 MB
Supplementary informationData, 17.5 MBTrwydded: CC BY

Cysylltiad parhaol

Dolen barhaus

Ffeiliau eraill a chysylltiadau

Dolen i’r cyhoeddiad yn Scopus

Gancho Slavov
- gas38aber.acuk
- Athrofa y Gwyddorau Biolegol, Amgylcheddol a Gwledig - Germinal Chair / Reader in Crop Genomics
Unigolyn: Dysgu ac Ymchwil

1 Wedi Gorffen

A population genomics approach to accelerating the domestication of the energy grass miscanthus
Slavov, G. (Prif Ymchwilydd)
Biotechnology and Biological Sciences Research Council
01 Ion 2014 → 31 Rhag 2016
Prosiect: Ymchwil a ariannwyd yn allanol

Dyfynnu hyn

@article{e762dfca1e9b40e58ab12e482cb8f934,

title = "Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations",

abstract = "Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation.",

keywords = "Adaptation, Physiological/genetics, British Columbia, Chromosome Mapping, Chromosomes, Plant/genetics, Evolution, Molecular, Gene Duplication, Genes, Plant/genetics, Genetic Variation, Genetics, Population, Genome, Plant/genetics, Genomics/methods, Genotype, Geography, Linkage Disequilibrium, Plant Proteins/genetics, Polymorphism, Single Nucleotide, Populus/classification, Selection, Genetic, Washington",

author = "Luke Evans and Gancho Slavov and Eli Rodgers-Melnick and Joel Martin and Priya Ranjan and Wellington Muchero and Brunner, {Amy M} and Wendy Schackwitz and Gunter, {Lee E.} and Jin-Gui Chen and Tuskan, {Gerald A.} and DiFazio, {Stephen P.}",

note = "Funding Information: We thank the members of BioEnergy Science Center for their varied contributions to this work, and especially those involved in the collection, propagation and maintenance of the common gardens, including G. Howe, A. Groover, R. Stettler, J. Johnson and the staff at Mt. Jefferson Farms and Greenwood Resources. We thank the West Virginia University High Performance Computing facility, in particular N. Gregg and M. Carlise. P. balsamifera transcriptomes were provided by M. Olson (Texas Tech University). This work was supported by funding from the BioEnergy Science Center, a US Department of Energy (DOE) Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. A.M.B. acknowledges support from the Virginia Agricultural Experiment Station and the McIntire Stennis Program of the National Institute of Food and Agriculture, US Department of Agriculture. Publisher Copyright: {\textcopyright} 2014 Nature America, Inc. All rights reserved.",

year = "2014",

month = sep,

day = "26",

doi = "10.1038/ng.3075",

language = "English",

volume = "46",

pages = "1089--1096",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Springer Nature",

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AU - Slavov, Gancho

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AU - Martin, Joel

AU - Ranjan, Priya

AU - Muchero, Wellington

AU - Brunner, Amy M

AU - Schackwitz, Wendy

AU - Gunter, Lee E.

AU - Chen, Jin-Gui

AU - Tuskan, Gerald A.

AU - DiFazio, Stephen P.

N1 - Funding Information: We thank the members of BioEnergy Science Center for their varied contributions to this work, and especially those involved in the collection, propagation and maintenance of the common gardens, including G. Howe, A. Groover, R. Stettler, J. Johnson and the staff at Mt. Jefferson Farms and Greenwood Resources. We thank the West Virginia University High Performance Computing facility, in particular N. Gregg and M. Carlise. P. balsamifera transcriptomes were provided by M. Olson (Texas Tech University). This work was supported by funding from the BioEnergy Science Center, a US Department of Energy (DOE) Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. A.M.B. acknowledges support from the Virginia Agricultural Experiment Station and the McIntire Stennis Program of the National Institute of Food and Agriculture, US Department of Agriculture. Publisher Copyright: © 2014 Nature America, Inc. All rights reserved.

PY - 2014/9/26

Y1 - 2014/9/26

N2 - Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation.

AB - Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation.

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KW - British Columbia

KW - Chromosome Mapping

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KW - Evolution, Molecular

KW - Gene Duplication

KW - Genes, Plant/genetics

KW - Genetic Variation

KW - Genetics, Population

KW - Genome, Plant/genetics

KW - Genomics/methods

KW - Genotype

KW - Geography

KW - Linkage Disequilibrium

KW - Plant Proteins/genetics

KW - Polymorphism, Single Nucleotide

KW - Populus/classification

KW - Selection, Genetic

KW - Washington

UR - http://www.scopus.com/inward/record.url?scp=84922055577&partnerID=8YFLogxK

U2 - 10.1038/ng.3075

DO - 10.1038/ng.3075

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VL - 46

SP - 1089

EP - 1096

JO - Nature Genetics

JF - Nature Genetics

IS - 10

ER -

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

Crynodeb

NDC y CU

Mynediad at Ddogfen

Cysylltiad parhaol

Ffeiliau eraill a chysylltiadau

Ôl bys

Proffiliau

Gancho Slavov

Prosiectau

A population genomics approach to accelerating the domestication of the energy grass miscanthus

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