Population genomics of the eastern cottonwood ( Populus deltoides )
Abstract
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 inmore »
- Authors:
-
[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
- Horticultural Sciences Department University of Florida Gainesville FL USA
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
- Biology Department University of Florida Gainesville FL USA
- Biology Department University of Florida Gainesville FL USA, University of Florida Genetics Institute University of Florida Gainesville FL USA
- 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)
- 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. https://doi.org/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. https://doi.org/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 = {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.},
doi = {10.1002/ece3.3466},
journal = {Ecology and Evolution},
number = 22,
volume = 7,
place = {United Kingdom},
year = {Tue Oct 10 00:00:00 EDT 2017},
month = {Tue Oct 10 00:00:00 EDT 2017}
}
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