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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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Autores principales: Fahrenkrog, Annette M., Neves, Leandro G., Resende, Márcio F. R., Dervinis, Christopher, Davenport, Ruth, Barbazuk, W. Brad, Kirst, Matias
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696417/
https://www.ncbi.nlm.nih.gov/pubmed/29187979
http://dx.doi.org/10.1002/ece3.3466
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author Fahrenkrog, Annette M.
Neves, Leandro G.
Resende, Márcio F. R.
Dervinis, Christopher
Davenport, Ruth
Barbazuk, W. Brad
Kirst, Matias
author_facet Fahrenkrog, Annette M.
Neves, Leandro G.
Resende, Márcio F. R.
Dervinis, Christopher
Davenport, Ruth
Barbazuk, W. Brad
Kirst, Matias
author_sort Fahrenkrog, Annette M.
collection PubMed
description 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 (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 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.
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spelling pubmed-56964172017-11-29 Population genomics of the eastern cottonwood (Populus deltoides) Fahrenkrog, Annette M. Neves, Leandro G. Resende, Márcio F. R. Dervinis, Christopher Davenport, Ruth Barbazuk, W. Brad Kirst, Matias Ecol Evol Original Research 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 (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 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. John Wiley and Sons Inc. 2017-10-10 /pmc/articles/PMC5696417/ /pubmed/29187979 http://dx.doi.org/10.1002/ece3.3466 Text en © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Fahrenkrog, Annette M.
Neves, Leandro G.
Resende, Márcio F. R.
Dervinis, Christopher
Davenport, Ruth
Barbazuk, W. Brad
Kirst, Matias
Population genomics of the eastern cottonwood (Populus deltoides)
title Population genomics of the eastern cottonwood (Populus deltoides)
title_full Population genomics of the eastern cottonwood (Populus deltoides)
title_fullStr Population genomics of the eastern cottonwood (Populus deltoides)
title_full_unstemmed Population genomics of the eastern cottonwood (Populus deltoides)
title_short Population genomics of the eastern cottonwood (Populus deltoides)
title_sort population genomics of the eastern cottonwood (populus deltoides)
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696417/
https://www.ncbi.nlm.nih.gov/pubmed/29187979
http://dx.doi.org/10.1002/ece3.3466
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