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

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

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253 Scopus citations

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
DOIs	https://doi.org/10.1038/ng.3075
State	Published - Sep 26 2014

Funding

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.

Funders	Funder number
BioEnergy Science Center
DOE Office of Science
Office of Biological and Environmental Research
US Department of Agriculture
US Department of Energy
U.S. Department of Energy
National Institute of Food and Agriculture
Alabama Agricultural Experiment Station
Biotechnology and Biological Sciences Research Council	BB/K01711X/1
Biotechnology and Biological Sciences Research Council

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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.",

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AU - Muchero, Wellington

AU - Brunner, Amy M.

AU - Schackwitz, Wendy

AU - Gunter, Lee

AU - Chen, Jin Gui

AU - Tuskan, Gerald A.

AU - Difazio, Stephen P.

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

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