Population genomics of the eastern cottonwood ( Populus deltoides )

Fahrenkrog, Annette M.; Neves, Leandro G.; Resende, Jr, Márcio F. R.; Dervinis, Christopher; Davenport, Ruth; Barbazuk, W. Brad; Kirst, Matias

doi:10.1002/ece3.3466

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

Journal Article · Tue Oct 10 00:00:00 EDT 2017 · Ecology and Evolution

DOI:https://doi.org/10.1002/ece3.3466· OSTI ID:1398844

^[1]; Neves, Leandro G. ^[1]; Resende, Jr, Márcio F. R. ^[2]; Dervinis, Christopher ^[3]; Davenport, Ruth ^[4]; Barbazuk, W. Brad ^[5]; Kirst, Matias ^[6]

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

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.

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Research Organization:: Univ. of Florida, Gainesville, FL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FG02-05ER64114; SC0003893

OSTI ID:: 1398844

Alternate ID(s):: OSTI ID: 1398845; OSTI ID: 1508795

Journal Information:: Ecology and Evolution, Journal Name: Ecology and Evolution Vol. 7 Journal Issue: 22; ISSN 2045-7758

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 27 works

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eastern cottonwood
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genetic diversity
local adaptation
population structure
Populus deltoides

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

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