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Title: Population genomics of the eastern cottonwood ( Populus deltoides )

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 ( 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 se-lection (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 ofmore » 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.« less

Authors:
ORCiD logo [1];  [1];  [2];  [3];  [4];  [5];  [6]
  1. School of Forest Resources and Conservation, University of Florida, Gainesville FL USA, Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville FL USA
  2. Horticultural Sciences Department, University of Florida, Gainesville FL USA
  3. School of Forest Resources and Conservation, University of Florida, Gainesville FL USA
  4. Biology Department, University of Florida, Gainesville FL USA
  5. Biology Department, University of Florida, Gainesville FL USA, University of Florida Genetics Institute, University of Florida, Gainesville FL USA
  6. School of Forest Resources and Conservation, University of Florida, Gainesville FL USA, University of Florida Genetics Institute, University of Florida, Gainesville FL USA
Publication Date:
Research Org.:
Univ. of Florida, Gainesville, FL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1398844
Alternate Identifier(s):
OSTI ID: 1398845; OSTI ID: 1508795
Grant/Contract Number:  
FG02-05ER64114; SC0003893
Resource Type:
Published Article
Journal Name:
Ecology and Evolution
Additional Journal Information:
Journal Name: Ecology and Evolution Journal Volume: 7 Journal Issue: 22; Journal ID: ISSN 2045-7758
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United Kingdom
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; eastern cottonwood; exome capture; genetic diversity; local adaptation; population structure; Populus deltoides

Citation Formats

Fahrenkrog, Annette M., Neves, Leandro G., Resende, Jr, Márcio F. R., Dervinis, Christopher, Davenport, Ruth, Barbazuk, W. Brad, and Kirst, Matias. Population genomics of the eastern cottonwood ( Populus deltoides ). United Kingdom: N. p., 2017. Web. doi:10.1002/ece3.3466.
Fahrenkrog, Annette M., Neves, Leandro G., Resende, Jr, Márcio F. R., Dervinis, Christopher, Davenport, Ruth, Barbazuk, W. Brad, & Kirst, Matias. Population genomics of the eastern cottonwood ( Populus deltoides ). United Kingdom. doi:10.1002/ece3.3466.
Fahrenkrog, Annette M., Neves, Leandro G., Resende, Jr, Márcio F. R., Dervinis, Christopher, Davenport, Ruth, Barbazuk, W. Brad, and Kirst, Matias. Tue . "Population genomics of the eastern cottonwood ( Populus deltoides )". United Kingdom. doi:10.1002/ece3.3466.
@article{osti_1398844,
title = {Population genomics of the eastern cottonwood ( Populus deltoides )},
author = {Fahrenkrog, Annette M. and Neves, Leandro G. and Resende, Jr, Márcio F. R. and Dervinis, Christopher and Davenport, Ruth and Barbazuk, W. Brad and Kirst, Matias},
abstractNote = {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 se-lection (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.},
doi = {10.1002/ece3.3466},
journal = {Ecology and Evolution},
number = 22,
volume = 7,
place = {United Kingdom},
year = {2017},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1002/ece3.3466

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