Population genomics of the eastern cottonwood (Populus deltoides)
Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated...
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Published in | Ecology and evolution Vol. 7; no. 22; pp. 9426 - 9440 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
John Wiley & Sons, Inc
01.11.2017
Wiley Blackwell (John Wiley & Sons) John Wiley and Sons Inc |
Subjects | |
Online Access | Get full text |
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Abstract | Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural P. deltoides population showed low levels of subpopulation differentiation (FST = 0.022–0.106), high genetic diversity (θW = 0.00100, π = 0.00170), a large effective population size (Ne ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D), subpopulation differentiation (XTX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.
Forest tree species are especially vulnerable to the effects of climate change, with their survival and adaptation capacity determined in part by their genetic makeup. Applying a combination of population genomics methods to uncover signatures of selection and discover genetic markers associated with the environment, we identified a set of candidate genes for adaptation in the eastern cottonwood (Populus deltoides). This species is relevant as a feedstock for wood products and bioenergy, as well as a key component of riparian ecosystems in North America. |
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AbstractList | Abstract
Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (
Populus deltoides
). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (
<styled-content style='fixed-case'>SNP</styled-content>
s). This natural
P. deltoides
population showed low levels of subpopulation differentiation (
F
ST
= 0.022–0.106), high genetic diversity (θ
W
= 0.00100, π = 0.00170), a large effective population size (
N
e
≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's
D
), subpopulation differentiation (
<styled-content style='fixed-case'>
X
T
X
</styled-content>
), and environmental association analyses with eleven climate variables carried out with two different methods (
<styled-content style='fixed-case'>LFMM</styled-content>
and
<styled-content style='fixed-case'>BAYENV</styled-content>
2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species,
Populus trichocarpa
, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in
P. deltoides
throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change. Abstract Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood ( Populus deltoides ). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms ( SNP s). This natural P. deltoides population showed low levels of subpopulation differentiation ( F ST = 0.022–0.106), high genetic diversity (θ W = 0.00100, π = 0.00170), a large effective population size ( N e ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D ), subpopulation differentiation ( X T X ), and environmental association analyses with eleven climate variables carried out with two different methods ( LFMM and BAYENV 2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa , indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change. Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural P. deltoides population showed low levels of subpopulation differentiation (FST = 0.022–0.106), high genetic diversity (θW = 0.00100, π = 0.00170), a large effective population size (Ne ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D), subpopulation differentiation (XTX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change. Forest tree species are especially vulnerable to the effects of climate change, with their survival and adaptation capacity determined in part by their genetic makeup. Applying a combination of population genomics methods to uncover signatures of selection and discover genetic markers associated with the environment, we identified a set of candidate genes for adaptation in the eastern cottonwood (Populus deltoides). This species is relevant as a feedstock for wood products and bioenergy, as well as a key component of riparian ecosystems in North America. Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural P. deltoides population showed low levels of subpopulation differentiation (FST = 0.022–0.106), high genetic diversity (θW = 0.00100, π = 0.00170), a large effective population size (Ne ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D), subpopulation differentiation (XTX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change. Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood ( ). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural population showed low levels of subpopulation differentiation ( = 0.022-0.106), high genetic diversity (θ = 0.00100, π = 0.00170), a large effective population size ( ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's ), subpopulation differentiation ( ), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, , indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change. Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood ( Populus deltoides ). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms ( SNP s). This natural P. deltoides population showed low levels of subpopulation differentiation ( F ST = 0.022–0.106), high genetic diversity (θ W = 0.00100, π = 0.00170), a large effective population size ( N e ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D ), subpopulation differentiation ( X T X ), and environmental association analyses with eleven climate variables carried out with two different methods ( LFMM and BAYENV 2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa , indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change. |
Author | Resende, Márcio F. R. Kirst, Matias Barbazuk, W. Brad Fahrenkrog, Annette M. Davenport, Ruth Neves, Leandro G. Dervinis, Christopher |
AuthorAffiliation | 2 Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA 5 University of Florida Genetics Institute University of Florida Gainesville FL USA 4 Biology Department University of Florida Gainesville FL USA 6 Present address: RAPiD Genomics LLC 756 2nd Avenue Gainesville FL 32601 USA 1 School of Forest Resources and Conservation University of Florida Gainesville FL USA 3 Horticultural Sciences Department University of Florida Gainesville FL USA |
AuthorAffiliation_xml | – name: 5 University of Florida Genetics Institute University of Florida Gainesville FL USA – name: 4 Biology Department University of Florida Gainesville FL USA – name: 2 Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA – name: 1 School of Forest Resources and Conservation University of Florida Gainesville FL USA – name: 3 Horticultural Sciences Department University of Florida Gainesville FL USA – name: 6 Present address: RAPiD Genomics LLC 756 2nd Avenue Gainesville FL 32601 USA |
Author_xml | – sequence: 1 givenname: Annette M. orcidid: 0000-0002-7553-6382 surname: Fahrenkrog fullname: Fahrenkrog, Annette M. organization: University of Florida – sequence: 2 givenname: Leandro G. surname: Neves fullname: Neves, Leandro G. organization: University of Florida – sequence: 3 givenname: Márcio F. R. surname: Resende fullname: Resende, Márcio F. R. organization: University of Florida – sequence: 4 givenname: Christopher surname: Dervinis fullname: Dervinis, Christopher organization: University of Florida – sequence: 5 givenname: Ruth surname: Davenport fullname: Davenport, Ruth organization: University of Florida – sequence: 6 givenname: W. Brad surname: Barbazuk fullname: Barbazuk, W. Brad organization: University of Florida – sequence: 7 givenname: Matias surname: Kirst fullname: Kirst, Matias email: mkirst@ufl.edu organization: University of Florida |
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Copyright | 2017 The Authors. published by John Wiley & Sons Ltd. 2017. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
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Keywords | exome capture Populus deltoides genetic diversity local adaptation eastern cottonwood population structure |
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Snippet | Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern... Abstract Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the... |
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StartPage | 9426 |
SubjectTerms | Adaptation BASIC BIOLOGICAL SCIENCES Biological evolution Breeding Climate change Differentiation eastern cottonwood Economic importance Environmental changes Environmental organizations ENVIRONMENTAL SCIENCES Evolution exome capture Genes Genetic diversity Genomics Identification methods Linkage disequilibrium local adaptation Original Research Plant breeding Poplar Population Population number population structure Population studies Populus deltoides Renewable energy Riparian environments Single-nucleotide polymorphism |
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Title | Population genomics of the eastern cottonwood (Populus deltoides) |
URI | https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fece3.3466 https://www.ncbi.nlm.nih.gov/pubmed/29187979 https://www.proquest.com/docview/1977882347 https://www.osti.gov/biblio/1398844 https://pubmed.ncbi.nlm.nih.gov/PMC5696417 |
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