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Climate change is one of the most important challenges for mankind in the far and near future. In this regard, sustainable production of woody crops on marginal land with low water availability is a major challenge to tackle. This dataset is part of an experiment, in which we exposed three genetically differentiated genotypes of Populus nigra originating from contrasting natural habitats to gradually increasing moderate drought. RNA sequencing was performed on fine roots, developing xylem and leaves of those three genotypes under control and moderate drought conditions in order to get a comprehensive dataset on the transcriptional changes at the whole plant level under water limiting conditions. This dataset has already provided insight in the transcriptional control of saccharification potential of the three Populus genotypes under drought conditions and we suggest that our data will be valuable for further in-depth analysis regarding candidate gene identification or, on a bigger scale, for meta-transcriptome analysis. Measurement(s) transcriptome Technology Type(s) illumina sequencing Factor Type(s) treatment Sample Characteristic - Organism Populus nigra Sample Characteristic - Environment greenhouse experiment [ABSTRACT FROM AUTHOR]

Background: Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species. Results: We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population. Conclusions: The three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species. [ABSTRACT FROM AUTHOR]

Dedicated non-food bioenergy crops like poplar are needed as sustainable, lowinput feedstocks for renewable energy in a future drier climate, where they can be grown on marginal soils. Such plants should have a low water, carbon, and chemical footprint. Capturing natural variation in traits associated with water use efficiency (WUE) is the first step to developing trees that require less water and may be adapted to drier environments. We have assessed stomatal conductance (gs) and leaf carbon isotope composition (δ13C, an indirect indicator of leaf WUE) in two Populus species, P. deltoides and P. trichocarpa and their F2 progeny, grown in the United Kingdom and in Italy. Populus deltoides leaves showed lower δ13C than P. trichocarpa, suggesting a higher WUE in P. trichocarpa, although without drought preconditioning, gs of P. trichocarpa was less responsive to dehydration and abscisic acid treatment than P. deltoides, suggesting that leaf anatomy may also contribute to δ13C in Populus. Quantitative trait loci (QTL) were identified for δ13C on eight linkage groups (LG) and two QTL for gs. From these. QTL and differential gene expression in response to drought from microarray data, we focused on three hotspots and identified 23 novel candidate genes on LG VI, X, and XVI. We have begun to unravel the genetic basis of WUE in bioenergy Populus revealing important underpinning data for breeding and improvement in poplar genotypes for a future drier climate. [ABSTRACT FROM AUTHOR]

Woody biomass produced from short rotation coppice ( SRC) poplar ( Populus spp.) and willow ( Salix spp.) is a bioenergy feedstock that can be grown widely across temperate landscapes and its use is likely to increase in future. Process-based models are therefore required to predict current and future yield potential that are spatially resolved and can consider new genotypes and climates that will influence future yield. The development of a process-based model for SRC poplar and willow, ForestGrowth- SRC, is described and the ability of the model to predict SRC yield and water use efficiency ( WUE) was evaluated. ForestGrowth- SRC was parameterized from a process-based model, ForestGrowth for high forest. The new model predicted annual above ground yield well for poplar ( r2 = 0.91, RMSE = 1.46 ODT ha−1 yr−1) and willow ( r2 = 0.85, RMSE = 1.53 ODT ha−1 yr−1), when compared with measured data from seven sites in contrasting climatic zones across the United Kingdom. Average modelled yields for poplar and willow were 10.3 and 9.0 ODT ha−1 yr−1, respectively, and interestingly, the model predicted a higher WUE for poplar than for willow: 9.5 and 5.5 g kg−1 respectively. Using regional mapped climate and soil inputs, modelled and measured yields for willow compared well ( r2 = 0.58, RMSE = 1.27 ODT ha−1 yr−1), providing the first UK map of SRC yield, from a process-based model. We suggest that the model can be used for predicting current and future SRC yields at a regional scale, highlighting important species and genotype choices with respect to water use efficiency and yield potential. [ABSTRACT FROM AUTHOR]

Relatively little is known about the transcriptional response or genetic control of response and adaptation of trees to tropospheric ozone exposure. Such understanding is needed as up to 50% of forests, globally, may be subjected to phytotoxic concentrations of ozone. The physiological, transcriptional and genetic response to ozone was examined in Populus trichocarpa and P. deltoides, which show extreme sensitivity and tolerance to ozone, respectively. Using an inbred F2 mapping population derived from these two species, we mapped quantitative trait loci (QTL) for traits associated with ozone response, examined segregation of the transcriptional response to ozone and co-located genes showing divergent responses between tolerant and sensitive genotypes with QTL. QTL were identified linking detrimental effects of ozone with leaf and biomass traits and differential responses were found for key genes involved in ethylene production and response. [Copyright &y& Elsevier]

• Limited information on likely supply and spatial yield of bioenergy crops exists for the UK. Here, productivities are reported of poplar ( Populus spp.) and willow ( Salix spp.) grown as short-rotation coppice (SRC), using data from a large 49-site yield trial network. • A partial least-squares regression technique was used to upscale actual field trial observations across England and Wales. Spatial productivity was then assessed under different land-use scenarios. • Mean modelled yields ranged between 4.9 and 10.7 oven-dry tonnes (odt) ha−1 yr−1. Yields were generally higher in willow than in poplar, reflecting the susceptibility of older poplar genotypes to rust and their tendency for single stem dominance. Replacing 10% of arable land, 20% of improved grassland and 100% of set-aside grassland in England and Wales with the three most productive genotypes would yield 13 Modt of biomass annually (supplying 7% of UK electricity production or 48% of UK combined heat and power (CHP) production). • Results show existing SRC genotypes have the immediate potential to be an important component of a mixed portfolio of renewables and that, in future, as new and improved genotypes become available, higher yields could extend this potential further. [ABSTRACT FROM AUTHOR]

The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response. [ABSTRACT FROM AUTHOR]

Limited information is available on the genetic variation and control for plant growth response to elevated CO2 (e[CO2]). Such information is necessary to understand plant adaptation and evolution in future rising CO2. Here, quantitative trait loci (QTL) for leaf growth, development, quality and leaf senescence were determined in a tree pedigree – an F2 hybrid of Populus trichocarpa T. & G and Populus deltoides Marsh, following season-long exposure to either current day ambient carbon dioxide (a[CO2]) or e[CO2] at 600 µL L−1. Leaf growth and development differed between the grandparents such that P. trichocarpa showed greater response to e[CO2]. In the F2 generation, leaf development and quality traits including leaf area, leaf shape, epidermal cell area, and stomatal number, specific leaf area (SLA), and the phenology trait, canopy senescence index, were sensitive to e[CO2]. Sixty-nine QTL were mapped for the 19 traits of plants in a[CO2] while 60 QTL were mapped for plants in e[CO2]. The results suggest that although many QTL mapped to common positions in a[CO2] and e[CO2], confirming their importance in determining growth, there was also differential genetic control for a number of traits including leaf senescence. Candidate genes were shown to collocate to regions where response QTL mapped. This study is the first to identify candidate genes that may be important in determining plant adaptation to future high-CO2 world. [ABSTRACT FROM AUTHOR]

The quickly rising atmospheric carbon dioxide (CO2)-levels, justify the need to explore all carbon (C) sequestration possibilities that might mitigate the current CO2 increase. Here, we report the likely impact of future increases in atmospheric CO2 on woody biomass production of three poplar species ( Populus alba L. clone 2AS-11, Populus nigra L. clone Jean Pourtet and Populus× euramericana clone I-214). Trees were growing in a high-density coppice plantation during the second rotation (i.e., regrowth after coppice; 2002–2004; POPFACE/EUROFACE). Six plots were studied, half of which were continuously fumigated with CO2 (FACE; free air carbon dioxide enrichment of 550 ppm). Half of each plot was fertilized to study the interaction between CO2 and nutrient fertilization. At the end of the second rotation, selective above- and belowground harvests were performed to estimate the productivity of this bio-energy plantation. Fertilization did not affect growth of the poplar trees, which was likely because of the high rates of fertilization during the previous agricultural land use. In contrast, elevated CO2 enhanced biomass production by up to 29%, and this stimulation did not differ between above- and belowground parts. The increased initial stump size resulting from elevated CO2 during the first rotation (1999–2001) could not solely explain the observed final biomass increase. The larger leaf area index after canopy closure and the absence of any major photosynthetic acclimation after 6 years of fumigation caused the sustained CO2-induced biomass increase after coppice. These results suggest that, under future CO2 concentrations, managed poplar coppice systems may exhibit higher potential for C sequestration and, thus, help mitigate climate change when used as a source of C-neutral energy. [ABSTRACT FROM AUTHOR]

• The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure ofPopulus ×  euramericana(clone I-214) to elevated[CO2] in a FACE (free-air CO2 enrichment) experiment.• Gene expression was sensitive to elevated[CO2] but the response depended on the developmental age of the leaves, and< 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated[CO2], while in semimature leaves most were downregulated in elevated[CO2].• For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed byanova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR.• This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.New Phytologist(2005)doi: 10.1111/j.1469-8137.2005.01450.x© New Phytologist(2005) [ABSTRACT FROM AUTHOR]

• The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure ofPopulus ×  euramericana(clone I-214) to elevated[CO2] in a FACE (free-air CO2 enrichment) experiment.• Gene expression was sensitive to elevated[CO2] but the response depended on the developmental age of the leaves, and< 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated[CO2], while in semimature leaves most were downregulated in elevated[CO2].• For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed byanova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR.• This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.New Phytologist(2005)doi: 10.1111/j.1469-8137.2005.01450.x© New Phytologist(2005) [ABSTRACT FROM AUTHOR]

Investigates the effects of elevated carbon dioxide on leaf development in three genotypes of Populus. Decline in the nitrogen content of leaf; Measurement of leaf production and longevity; Impact of elevated carbon dioxide on plant epidermal cells.

Examines the effects of free-air carbon dioxide (CO [sub 2]) enrichment on the leaves of the fast-growing tree Populus X euramericana. Influence of increased cell expansion and cell production to the effects of elevated (CO [sub 2]); Exhibition of basipetal gradient of leaf development; Importance of rate and timing of cell production in determining leaf size.

Trees are used to produce a variety of wood‐based products including timber, pulp and paper. More recently, their use as a source of renewable energy has also been highlighted, as has their value for carbon mitigation within the Kyoto Protocol. Relative to food crops, the domestication of trees has only just begun; the long generation time and complex nature of juvenile and mature growth forms are contributory factors. To accelerate domestication, and to understand further some of the unique processes that occur in woody plants such as dormancy and secondary wood formation, a ‘model’ tree is needed. Here it is argued that Populus is rapidly becoming accepted as the ‘model’ woody plant and that such a ‘model’ tree is necessary to complement the genetic resource being developed in arabidopsis. The genus Populus (poplars, cottonwoods and aspens) contains approx. 30 species of woody plant, all found in the Northern hemisphere and exhibiting some of the fastest growth rates observed in temperate trees. Populus is fulfilling the ‘model’ role for a number of reasons. First, and most important, is the very recent commitment to sequence the Populus genome, a project initiated in February 2002. This will be the first woody plant to be sequenced. Other reasons include the relatively small genome size (450–550 Mbp) of Populus, the large number of molecular genetic maps and the ease of genetic transformation. Populus may also be propagated vegetatively, making mapping populations immortal and facilitating the production of large amounts of clonal material for experimentation. Hybridization occurs routinely and, in these respects, Populus has many similarities to arabidopsis. However, Populus also differs from arabidopsis in many respects, including being dioecious, which makes selfing and back‐cross manipulations impossible. The long time‐to‐flower is also a limitation, whilst physiological and biochemical experiments are more readily conducted in Populus compared with the small‐statured arabidopsis. Recent advances in the development of large expressed sequence tagged collections, microarray analysis and the free distribution of mapping pedigrees for quantitative trait loci analysis secure Populus as the ideal subject for further exploitation by a wide range of scientists including breeders, physiologists, biochemists and molecular biologists. In addition, and in contrast to other model plants, the genus Populus also has genuine commercial value as a tree for timber, plywood, pulp and paper. [ABSTRACT FROM PUBLISHER]

Genetic variation in stomatal initiation and density, and epidermal cell size and number were examined in a hybrid pedigree of Populus trichocarpa T. & G. and P. deltoides Marsh in both ambient ([aCO2]) and elevated ([eCO2]) concentrations of CO2. We aimed to link anatomical traits with the underlying genetic map of F2 Family 331, composed of 350 markers across 19 linkage groups. Leaf stomatal and epidermal cell traits showed pronounced differences between the original parents. We considered the following traits in the F2 population: stomatal density (SD), stomatal index (SI), epidermal cell area (ECA) and the number of epidermal cells per leaf (ECN). In [eCO2], adaxial SD and SI were reduced in the F2 population, whereas ECA increased and ECN remained unchanged. In [aCO2], four putative quantitative trait loci (QTL) with logarithm of the odds ratio (LOD) scores greater than 2.9 were found for stomatal traits on linkage group B: adaxial SI (LOD scores of 5.4 and 5.2); abaxial SI (LOD score of 3.3); and SD (LOD score of 3.2). These results imply that QTL for SI and SD share linkage group B and are under genetic control. More moderate LOD scores (LOD scores >/= 2.5) suggest QTL for SI on linkage groups A and B and for SD on linkage groups B, D and X with a probable co-locating quantitative trait locus for SI and SD on linkage group D (position 46.3 cM). The QTL in both [aCO2] and [eCO2] for adaxial SD were co-located on linkage group X (LOD scores of 3.5 and 2.6, respectively) indicating a similar response across both treatments. Putative QTL were located on linkage group A (position 89.2 cM) for both leaf size and ECN in [aCO2] and for ECA at almost the same position. The data provide preliminary evidence that leaf stomatal and cell traits are amenable to QTL analysis. [ABSTRACT FROM PUBLISHER]

Leaf extension was stimulated following exposure of three interamerican hybrid poplar clones (Populus trichocarpa × P. deltoides); 'Unal', 'Boelare', and 'Beaupre' and a euramerican clone 'Primo' (Populus nigra × P. deltoides) to elevated CO2 in controlled environment chambers. For all three interamerican clones the evidence suggests that this was the result of increased leaf cell expansion associated with enhanced cell wall extensibility (WEx), measured as tensiometric increases in cell wall plasticity. For the interamerican clone 'Boelare', there was also a significant increase in cell wall elasticity following exposure to elevated CO2 (P ≤ 0.001). The effect of elevated CO2 in stimulating cell wall extensibility was confirmed in a detailed spatial analysis of extensibility made across the lamina of expanding leaves of the clone 'Boelare. For two of the interamerican hybrids, 'Unal' and 'Beaupre', both leaf cell water potential (ψ) and turgor pressure (P) were lower in elevated than in ambient CO2. By contrast, no significant effects on the cell wall properties or leaf water relations for the euramerican hybrid 'Primo' were observed following exposure to elevated CO2, suggesting that the mechanism for increased leaf extension in elevated CO2 differed, depending on clone. The cumulative total length of leaves of 'Boelare' grown in elevated CO2 was significantly increased (P ≤ 0.05) and since leaf number was not significantly increased in any inter-american clone it is hypothesized that final leaf size was stimulated in elevated CO2 for these clones. By contrast, there was no significant effect of CO2 on cumulative total leaf length for the euramerican clone 'Primo', but leaf number was significantly increased by elevated CO2. [ABSTRACT FROM AUTHOR]

Leaf extension was stimulated following exposure of three interamerican hybrid poplar clones (Populus trichocarpa × P. deltoides); 'Unal', 'Boelare', and 'Beaupre' and a euramerican clone 'Primo' (Populus nigra × P. deltoides) to elevated CO2 in controlled environment chambers. For all three interamerican clones the evidence suggests that this was the result of increased leaf cell expansion associated with enhanced cell wall extensibility (WEx), measured as tensiometric increases in cell wall plasticity. For the interamerican clone 'Boelare', there was also a significant increase in cell wall elasticity following exposure to elevated CO2 (P ≤ 0.001). The effect of elevated CO2 in stimulating cell wall extensibility was confirmed in a detailed spatial analysis of extensibility made across the lamina of expanding leaves of the clone 'Boelare. For two of the interamerican hybrids, 'Unal' and 'Beaupre', both leaf cell water potential (ψ) and turgor pressure (P) were lower in elevated than in ambient CO2. By contrast, no significant effects on the cell wall properties or leaf water relations for the euramerican hybrid 'Primo' were observed following exposure to elevated CO2, suggesting that the mechanism for increased leaf extension in elevated CO2 differed, depending on clone. The cumulative total length of leaves of 'Boelare' grown in elevated CO2 was significantly increased (P ≤ 0.05) and since leaf number was not significantly increased in any inter-american clone it is hypothesized that final leaf size was stimulated in elevated CO2 for these clones. By contrast, there was no significant effect of CO2 on cumulative total leaf length for the euramerican clone 'Primo', but leaf number was significantly increased by elevated CO2. [ABSTRACT FROM AUTHOR]

We examined the response of hybrid poplar to elevated CO2in contrasting growth environments: controlled environment chamber (CE), open-top chamber (OTC) and poplar free air CO2 enrichment (POPFACE) in order to compare short versus long-term effects andto determine whether generalisations in response are possible for this fast growing tree. Leaf growth, which for poplar is an important determinant of stemwood productivity was followed in all environments,as were the determinants of leaf growth//cell expansion and cell production. Elevated CO2 (550/700 Mumol mol-1, depending on environment) resulted in an increase in final leaf size forPopulus trichocarpax Populus deltoides (Populusx interamericana) andP. deltoidesx Populus nigra (Populusx euramericana), irrespective ofwhether plants were exposed during a short-term CE glasshouse study (90 days), a long-term OTC experiment (3 years) or during the first year of a POPFACE experiment. An exception was observed in the closed canopy POPFACE experiment, where final leaf size remained unaltered by CO2. Increased leaf extension rate was observed in elevated CO2 in all experiments, at some point during leaf development, as determined by leaf length. Again the exception were the POPFACE experiment, where effects were not statistically significant. Leaf production and specific leaf area (SLA) were increased and decreased, respectively, on five out of six occasions, although both were only statistically significant on two occasions and interestingly forSLA never in the FACE experiment. Although both cell expansion and cell production were sensitive to CO2 concentration, effects appeared highly dependent on growth environment and genotype. However, increased leaf cell expansion in elevated CO2 was often associated with changes in the biophysical properties of the cell wall, usually increased cell wall plasticity. This research has shown that en [ABSTRACT FROM AUTHOR]

Limited information is available on the genetic variation and control for plant growth response to elevated CO2 (e[CO2]). Such information is necessary to understand plant adaptation and evolution in future rising CO2. Here, quantitative trait loci (QTL) for leaf growth, development, quality and leaf senescence were determined in a tree pedigree – an F2 hybrid of Populus trichocarpa T. & G and Populus deltoides Marsh, following season-long exposure to either current day ambient carbon dioxide (a[CO2]) or e[CO2] at 600 µL L−1. Leaf growth and development differed between the grandparents such that P. trichocarpa showed greater response to e[CO2]. In the F2 generation, leaf development and quality traits including leaf area, leaf shape, epidermal cell area, and stomatal number, specific leaf area (SLA), and the phenology trait, canopy senescence index, were sensitive to e[CO2]. Sixty-nine QTL were mapped for the 19 traits of plants in a[CO2] while 60 QTL were mapped for plants in e[CO2]. The results suggest that although many QTL mapped to common positions in a[CO2] and e[CO2], confirming their importance in determining growth, there was also differential genetic control for a number of traits including leaf senescence. Candidate genes were shown to collocate to regions where response QTL mapped. This study is the first to identify candidate genes that may be important in determining plant adaptation to future high-CO2 world. [ABSTRACT FROM AUTHOR]