Project description:The complete chloroplast genome of <i>Populus deltoides</i> was characterized by reference-based assembly using whole-genome sequencing data. The total chloroplast genome size of <i>Populus deltoides</i> included a pair of inverted repeat regions (IRs) of 27,649?bp each, a small single-copy region (SSC) of 16,563?bp, and large single-copy region (LSC) of 85,096?bp, which was 156,957?bp in length. A total of 109 genes were predicted from the chloroplast genome, including 83 protein-coding genes, 22 <i>tRNA</i> genes, and four <i>rRNA</i> genes. The GC content of chloroplast genome for <i>Populus deltoides</i> was 36.68%. The phylogenetic analysis based on the reported chloroplast genomes of <i>Populus</i> showed that the chloroplast of the <i>Populus deltoides</i> is most closely related to the <i>Populus fremontii</i>. The complete chloroplast genome of <i>Populus deltoides</i> provides new insights into <i>Populus</i> evolutionary and genomic studies.
Project description:BACKGROUND AND AIMS:The use of woody crops for Quad-level (approx. 1 × 1018 J) energy production will require marginal agricultural lands that experience recurrent periods of water stress. Populus species have the capacity to increase dehydration tolerance by lowering osmotic potential via osmotic adjustment. The aim of this study was to investigate how the inherent genetic potential of a Populus clone to respond to drought interacts with the nature of the drought to determine the degree of biochemical response. METHODS:A greenhouse drought stress study was conducted on Populus deltoides 'WV94' and the resulting metabolite profiles of leaves were determined by gas chromatography-mass spectrometry following trimethylsilylation for plants subjected to cyclic mild (-0.5 MPa pre-dawn leaf water potential) drought vs. cyclic severe (-1.26 MPa) drought in contrast to well-watered controls (-0.1 MPa) after two or four drought cycles, and in contrast to plants subjected to acute drought, where plants were desiccated for up to 8 d. KEY RESULTS:The nature of drought (cyclic vs. acute), frequency of drought (number of cycles) and the severity of drought (mild vs. severe) all dictated the degree of osmotic adjustment and the nature of the organic solutes that accumulated. Whereas cyclic drought induced the largest responses in primary metabolism (soluble sugars, organic acids and amino acids), acute onset of prolonged drought induced the greatest osmotic adjustment and largest responses in secondary metabolism, especially populosides (hydroxycinnamic acid conjugates of salicin). CONCLUSIONS:The differential adaptive metabolite responses in cyclic vs. acute drought suggest that stress acclimation occurs via primary metabolism in response to cyclic drought, whereas expanded metabolic plasticity occurs via secondary metabolism following severe, acute drought. The shift in carbon partitioning to aromatic metabolism with the production of a diverse suite of higher order salicylates lowers osmotic potential and increases the probability of post-stress recovery.
Project description: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 (?W = 0.00100, ? = 0.00170), a large effective population size (Ne ? 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.
Project description:A microarray analysis of whole-genome gene expression in leaves was carried out in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Resultant data contributed to the analysis of the genetic architecture of gene expression in leaves of Populus. Overall design: Data include one biological replicate of 183 individuals segregating from a pseudo-backcross pedigree of (Populus trichocarpa X Populus deltoides) X Populus deltoides analyzed for gene expression (GE) in roots using one probe per gene for 55793 independent gene models (probes E_POPLARSxxxxxPxxxxx) and single feature sequence polymorphism (SFP) using one probe per gene for 12084 independent gene models (probes G_POPLARSxxxxxPxxxxx). GE and SFP probes were selected from 6-7 probes per gene previously tested in a pilot study of the two parent trees of the cross (Populus deltoides X Populus trichocarpa)