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 (θW = 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 (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.

Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

“…Most of the individuals distributed in the Mississippi River Basin were grouped together (Group II, Fig. 4a, c), and individuals in different states of the Mississippi River Basin had high genetic similarity, which was consistent with the results of Fahrenkrog et al [29,37]. The genetic differentiation between different basins indicated that geographical isolation restricts gene 10 exchange among populations [38].…”

“…The results showed that the P. deltoides population had abundant genetic diversity and moderate genetic differentiation. The results showed that the degree of genetic differentiation was relatively high, probably because the materials in this study were from three basins in the main distribution area of P. deltoides, and the materials in Fahrenkrog's study were mainly from the Mississippi River Basin [29,37]. Our research also showed that geographical isolation hindered gene exchange among individuals from different provenances and aggravated genetic differentiation.…”

“…Fahrenkrog et al performed the first population genomics study for 425 unrelated individuals of P. deltoides distributed in 13 states of the southeastern United States. By assessing population structure, population differentiation, genetic diversity and adaptation in P. deltoides, they found that the differentiation between subpopulations of the natural P. deltoides population was weak (F st = 0.022-0.106); however, the genetic diversity was high [29]. Furthermore, genome-wide association studies (GWASs) were also used to dissect the genetic regulation of eight growth and wood composition traits in P. deltoides, and single-nucleotide polymorphisms were detected by targeted resequencing of 18,153 genes in a population of 391 unrelated individuals.…”

“…Fahrenkrog et al [29] reported the first population genomics study for P. deltoides distributed in the Mississippi River Basin to determine their genetic diversity and adaptation. In the present study, we collected 384 individuals of P. deltoides preserved in the germplasm bank, which were originally distributed in 27 collection sites for 6 provenances.…”

Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

“…Fahrenkrog et al [29] reported the first population genomics study for P. deltoides distributed in the Mississippi River Basin to determine its genetic diversity and adaptation potential. In the present study, we analyzed 384 P. deltoides individuals preserved in the germplasm bank, which were originally distributed in 27 collection sites for 6 provenances.…”