Open AccessPopulation genomics of the eastern cottonwood ( Populus deltoides )
Author(s) -
Fahrenkrog Annette M.,
Neves Leandro G.,
Resende Márcio F. R.,
Dervinis Christopher,
Davenport Ruth,
Barbazuk W. Brad,
Kirst Matias
Publication year - 2017
Publication title -
ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.17
H-Index - 63
ISSN - 2045-7758
DOI - 10.1002/ece3.3466
Subject(s) - biology , populus trichocarpa , local adaptation , population genomics , genetic diversity , linkage disequilibrium , population , effective population size , genomics , evolutionary biology , adaptation (eye) , ecology , genetic variation , single nucleotide polymorphism , genetics , genome , gene , genotype , demography , neuroscience , sociology
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.