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

Department of Life Sciences

Research output: Contribution to journal › Article › peer-review

250 Citations (Scopus)

738 Downloads (Pure)

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.

Original language	English
Pages (from-to)	1089-1096
Number of pages	8
Journal	Nature Genetics
Volume	46
Issue number	10
Early online date	24 Aug 2014
DOIs	https://doi.org/10.1038/ng.3075
Publication status	Published - 26 Sept 2014

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/ng.3075

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associationsAccepted author manuscript, 1.97 MB
Supplementary informationData, 17.5 MBLicence: CC BY

Permanent link

Persistent link

Cite this

@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",

number = "10",

}

TY - JOUR

T1 - Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

AU - Evans, Luke

AU - Slavov, Gancho

AU - Rodgers-Melnick, Eli

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.

KW - Adaptation, Physiological/genetics

KW - British Columbia

KW - Chromosome Mapping

KW - Chromosomes, Plant/genetics

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

M3 - Article

C2 - 25151358

SN - 1061-4036

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

Abstract

Keywords

UN SDGs

Access to Document

Permanent link

Other files and links

Fingerprint

Gancho Slavov

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

Cite this

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

Abstract

Keywords

UN SDGs

Access to Document

Permanent link

Other files and links

Fingerprint

Profiles

Gancho Slavov

Projects

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

Cite this