The transcriptome of Populus in elevated CO2

A gene regulatory network in Arabidopsis roots reveals features and regulators of the plant response to elevated CO2

The elevation of CO₂ in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO₂ on plant growth and physiology, and to identify its regulatory in the roots, we analyzed genome expression in Arabidopsis roots through a combinatorial design with contrasted levels of CO₂ , nitrate, and iron. We demonstrated that elevated CO₂ has a modest effect on root genome expression under nutrient sufficiency, but by contrast leads to massive expression changes under nitrate or iron deficiencies. We demonstrated that elevated CO₂ negatively targets nitrate and iron starvation modules at the transcriptional level, associated with a reduction in high-affinity nitrate uptake. Finally, we inferred a gene regulatory network governing the root response to elevated CO₂ . This network allowed us to identify candidate transcription factors including MYB15, WOX11, and EDF3 which we experimentally validated for their role in the stimulation of growth by elevated CO₂ . Our approach identified key features and regulators of the plant response to elevated CO₂ , with the objective of developing crops resilient to climate change.

The decline of plant mineral nutrition under rising CO2: physiological and molecular aspects of a bad deal

The elevation of atmospheric CO₂ concentration has a strong impact on the physiology of C3 plants, far beyond photosynthesis and C metabolism. In particular, it reduces the concentrations of most mineral nutrients in plant tissues, posing major threats on crop quality, nutrient cycles, and carbon sinks in terrestrial agro-ecosystems. The causes of the detrimental effect of high CO₂ levels on plant mineral status are not understood. We provide an update on the main hypotheses and review the increasing evidence that, for nitrogen, this detrimental effect is associated with direct inhibition of key mechanisms of nitrogen uptake and assimilation. We also mention promising strategies for identifying genotypes that will maintain robust nutrient status in a future high-CO₂ world.

Physiological and Molecular Responses of Woody Plants Exposed to Future Atmospheric CO2 Levels under Abiotic Stresses

Climate change is mainly driven by the accumulation of carbon dioxide (CO2) in the atmosphere in the last century. Plant growth is constantly challenged by environmental fluctuations including heat waves, severe drought and salinity, along with ozone accumulation in the atmosphere. Food security is at risk in an increasing world population, and it is necessary to face the current and the expected effects of global warming. The effects of the predicted environment scenario of elevated CO2 concentration (e[CO2]) and more severe abiotic stresses have been scarcely investigated in woody plants, and an integrated view involving physiological, biochemical and molecular data is missing. This review highlights the effects of elevated CO2 in the metabolism of woody plants and the main findings of its interaction with abiotic stresses, including a molecular point of view, aiming to improve the understanding of how woody plants will face the predicted environmental conditions. Overall, e[CO2] stimulates photosynthesis and growth and attenuates mild to moderate abiotic stress in woody plants if root growth and nutrients are not limited. Moreover, e[CO2] does not induce acclimation in most tree species. Some high-throughput analyses involving omics techniques were conducted to better understand how these processes are regulated. Finally, knowledge gaps in the understanding of how the predicted climate condition will affect woody plant metabolism were identified, with the aim of improving the growth and production of this plant species.

Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]

As atmospheric [CO₂] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO₂ (eCO₂) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO₂. Although many genes were found to be commonly expressed by the two genotypes under eCO₂, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO₂. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO₂ with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO₂ in these coffee genotypes.

Effect of small coding genes on the circadian rhythms under elevated CO2 conditions in plants

Increase in atmospheric carbon dioxide (CO₂) has a significant effect on plant growth and development. To explore the elevated-CO₂ response, we generated transcriptional profiles over a time course (2 h-14 days) of exposure to elevated CO₂ in Arabidopsis thaliana. Genes related to photosynthesis were down-regulated and circadian rhythm-related genes were abnormally regulated in the early to middle phase of elevated CO₂ exposure. To understand the novel mechanism of elevated CO₂ signaling, we focused on 42 unknown small coding genes that showed differential expression patterns under elevated CO₂ conditions. Four transgenic plants overexpressing the small coding gene exhibited a growth-defective phenotype under elevated CO₂ but not under current CO₂. Transcriptome analysis showed that circadian rhythm-related genes were commonly regulated in four transgenic plants. These circadian rhythm-related genes were transcribed in the dark when CO₂ concentrations in the leaf was high. Taken together, our identified four small coding genes are likely to participate in elevated CO₂ signaling to the circadian rhythm.

Photosynthesis and yield response to elevated CO2, C4 plant foxtail millet behaves similarly to C3 species

Foxtail millet (Setaria italica) is a nutrient-rich food source traditionally grown in arid and semi-arid areas, as it is well adapted to drought climate. Yet there is limited information as how the crop responses to the changing climate. In order to investigate the response of foxtail millet to elevated [CO₂] and the underlying mechanism, the crop was grown at ambient [CO₂] (400 μmol mol^-1) and elevated [CO₂] (600 μmol mol^-1) in an open-top chamber (OTC) experimental facility in North China. The changes in leaf photosynthesis, chlorophyll fluorescence, biomass, yield and global gene expression in response to elevated [CO₂] were determined. Despite foxtail millet being a C₄ photosynthetic crop, photosynthetic rates (P_N) and intrinsic water-use efficiency (WUEi), were increased under elevated [CO₂]. Similarly, grain yield and above-ground biomass also significantly increased (P <  0.05) for the two years of experimentation under elevated [CO₂]. Increases in seeds and tiller number, spike and stem weight were the main contributors to the increased grain yield and biomass. Using transcriptomic analyses, this study further identified some genes which play a role in cell wall reinforcement, shoot initiation, stomatal conductance, carbon fixation, glycolysis / gluconeogenesis responsive to elevated [CO₂]. Changes in these genes reduced plant height, increased stem diameters, and promote CO₂ fixation. Higher photosynthetic rates at elevated [CO₂] demonstrated that foxtail millet was not photosynthetically saturated at elevated [CO₂] and its photosynthesis response to elevated [CO₂] were analogous to C₃ plants.

New insights into the cellular mechanisms of plant growth at elevated atmospheric carbon dioxide concentrations

Rising atmospheric carbon dioxide concentration ([CO₂ ]) significantly influences plant growth, development, and biomass. Increased photosynthesis rate, together with lower stomatal conductance, has been identified as the key factors that stimulate plant growth at elevated [CO₂ ] (e[CO₂ ]). However, variations in photosynthesis and stomatal conductance alone cannot fully explain the dynamic changes in plant growth. Stimulation of photosynthesis at e[CO₂ ] is always associated with post-photosynthetic secondary metabolic processes that include carbon and nitrogen metabolism, cell cycle functions, and hormonal regulation. Most studies have focused on photosynthesis and stomatal conductance in response to e[CO₂ ], despite the emerging evidence of e[CO₂ ]'s role in moderating secondary metabolism in plants. In this review, we briefly discuss the effects of e[CO₂ ] on photosynthesis and stomatal conductance and then focus on the changes in other cellular mechanisms and growth processes at e[CO₂ ] in relation to plant growth and development. Finally, knowledge gaps in understanding plant growth responses to e[CO₂ ] have been identified with the aim of improving crop productivity under a CO₂ rich atmosphere.

Prescreening in large populations as a tool for identifying elevated CO2-responsive genotypes in plants

Elevated atmospheric CO2 concentration (e[CO2]) can stimulate the photosynthesis and productivity of C3 species including food and forest crops. Intraspecific variation in responsiveness to e[CO2] can be exploited to increase productivity under e[CO2]. However, active selection of genotypes to increase productivity under e[CO2] is rarely performed across a wide range of germplasm, because of constraints of space and the cost of CO2 fumigation facilities. If we are to capitalise on recent advances in whole genome sequencing, approaches are required to help overcome these issues of space and cost. Here, we discuss the advantage of applying prescreening as a tool in large genome×e[CO2] experiments, where a surrogate for e[CO2] was used to select cultivars for more detailed analysis under e[CO2] conditions. We discuss why phenotypic prescreening in population-wide screening for e[CO2] responsiveness is necessary, what approaches could be used for prescreening for e[CO2] responsiveness, and how the data can be used to improve genetic selection of high-performing cultivars. We do this within the framework of understanding the strengths and limitations of genotype-phenotype mapping.

Genomewide transcriptional reprogramming in the seagrass Cymodocea nodosa under experimental ocean acidification

Here, we report the first use of massive-scale RNA-sequencing to explore seagrass response to CO₂ -driven ocean acidification (OA). Large-scale gene expression changes in the seagrass Cymodocea nodosa occurred at CO₂ levels projected by the end of the century. C. nodosa transcriptome was obtained using Illumina RNA-Seq technology and de novo assembly, and differential gene expression was explored in plants exposed to short-term high CO₂ /low pH conditions. At high pCO₂ , there was a significant increased expression of transcripts associated with photosynthesis, including light reaction functions and CO₂ fixation, and also to respiratory pathways, specifically for enzymes involved in glycolysis, in the tricarboxylic acid cycle and in the energy metabolism of the mitochondrial electron transport. The upregulation of respiratory metabolism is probably supported by the increased availability of photosynthates and increased energy demand for biosynthesis and stress-related processes under elevated CO₂ and low pH. The upregulation of several chaperones resembling heat stress-induced changes in gene expression highlighted the positive role these proteins play in tolerance to intracellular acid stress in seagrasses. OA further modifies C. nodosa secondary metabolism inducing the transcription of enzymes related to biosynthesis of carbon-based secondary compounds, in particular the synthesis of polyphenols and isoprenoid compounds that have a variety of biological functions including plant defence. By demonstrating which physiological processes are most sensitive to OA, this research provides a major advance in the understanding of seagrass metabolism in the context of altered seawater chemistry from global climate change.

A synthesis of the effects of atmospheric carbon dioxide enrichment on plant hydraulics: implications for whole-plant water use efficiency and resistance to drought

Here, we summarize studies on the effects of elevated [CO₂ ] (CO₂^e ) on the structure and function of plant hydraulic architecture and explore the implications of those changes using a model. Changes in conduit diameter and hydraulic conductance due to CO₂^e vary among species. Ring-porous species tend towards an increase in conduit size and consequently conductivity. The effect in diffuse-porous species is much more limited. In conifers, the results are mixed, some species show minor changes in xylem structure, while other studies found increases in tracheid density and diameter. Non-woody plants generally exhibited the reverse pattern with narrower conduits and lower hydraulic conductivity under CO₂^e . Further, changes in drought-resistance traits suggest that non-woody plants were the most affected by CO₂^e , which may permit them to better resist drought-induced embolism under future conditions. Due to their complexity, acclimation in hydraulic traits in response to CO₂^e is difficult to interpret when relying solely on measurements. When we examined how the observed tissues-specific trends might alter plant function, our modelling results suggest that these hydraulic changes would lead to reduced conductance and more frequent drought stress in trees that develop under CO₂^e with a more pronounced effect in isohydric than in anisohydric species.

Plant adaptation or acclimation to rising CO2 ? Insight from first multigenerational RNA-Seq transcriptome

Atmospheric carbon dioxide (CO₂ ) directly determines the rate of plant photosynthesis and indirectly effects plant productivity and fitness and may therefore act as a selective pressure driving evolution, but evidence to support this contention is sparse. Using Plantago lanceolata L. seed collected from a naturally high CO₂ spring and adjacent ambient CO₂ control site, we investigated multigenerational response to future, elevated atmospheric CO₂ . Plants were grown in either ambient or elevated CO₂ (700 μmol mol^-1 ), enabling for the first time, characterization of the functional and population genomics of plant acclimation and adaptation to elevated CO₂ . This revealed that spring and control plants differed significantly in phenotypic plasticity for traits underpinning fitness including above-ground biomass, leaf size, epidermal cell size and number and stomatal density and index. Gene expression responses to elevated CO₂ (acclimation) were modest [33-131 genes differentially expressed (DE)], whilst those between control and spring plants (adaptation) were considerably larger (689-853 DE genes). In contrast, population genomic analysis showed that genetic differentiation between spring and control plants was close to zero, with no fixed differences, suggesting that plants are adapted to their native CO₂ environment at the level of gene expression. An unusual phenotype of increased stomatal index in spring but not control plants in elevated CO₂ correlated with altered expression of stomatal patterning genes between spring and control plants for three loci (YODA, CDKB1;1 and SCRM2) and between ambient and elevated CO₂ for four loci (ER, YODA, MYB88 and BCA1). We propose that the two positive regulators of stomatal number (SCRM2) and CDKB1;1 when upregulated act as key controllers of stomatal adaptation to elevated CO₂ . Combined with significant transcriptome reprogramming of photosynthetic and dark respiration and enhanced growth in spring plants, we have identified the potential basis of plant adaptation to high CO₂ likely to occur over coming decades.

Genetic manipulation of putrescine biosynthesis reprograms the cellular transcriptome and the metabolome

BACKGROUND

With the increasing interest in metabolic engineering of plants using genetic manipulation and gene editing technologies to enhance growth, nutritional value and environmental adaptation, a major concern is the potential of undesirable broad and distant effects of manipulating the target gene or metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these two techniques with plant cell cultures to analyze the effects of genetic manipulation of a single step in the biosynthesis of polyamines because of their well-known roles in plant growth, development and stress responses.

RESULTS

The transcriptomes and metabolomes of a control and a high putrescine (HP) producing cell line of poplar (Populus nigra x maximowiczii) were compared using microarrays and GC/MS. The HP cells expressed an ornithine decarboxylase transgene and accumulated several-fold higher concentrations of putrescine, with only small changes in spermidine and spermine. The results show that up-regulation of a single step in the polyamine biosynthetic pathway (i.e. ornithine → putrescine) altered the expression of a broad spectrum of genes; many of which were involved in transcription, translation, membrane transport, osmoregulation, shock/stress/wounding, and cell wall metabolism. More than half of the 200 detected metabolites were significantly altered (p ≤ 0.05) in the HP cells irrespective of sampling date. The most noteworthy differences were in organic acids, carbohydrates and nitrogen-containing metabolites.

CONCLUSIONS

The results provide valuable information about the role of polyamines in regulating nitrogen and carbon use pathways in cell cultures of high putrescine producing transgenic cells of poplar vs. their low putrescine counterparts. The results underscore the complexity of cellular responses to genetic perturbation of a single metabolic step related to nitrogen metabolism in plants. Combined with recent studies from our lab, where we showed that higher putrescine production caused an increased flux of glutamate into ornithine concurrent with enhancement in glutamate production via additional nitrogen and carbon assimilation, the results from this study provide guidance in designing transgenic plants with increased nitrogen use efficiency, especially in plants intended for non-food/feed applications (e.g. increased biomass production for biofuels).

Changes in Air CO₂ Concentration Differentially Alter Transcript Levels of NtAQP1 and NtPIP2;1 Aquaporin Genes in Tobacco Leaves

The aquaporin specific control on water versus carbon pathways in leaves is pivotal in controlling gas exchange and leaf hydraulics. We investigated whether Nicotiana tabacum aquaporin 1 (NtAQP1) and Nicotiana tabacum plasma membrane intrinsic protein 2;1 (NtPIP2;1) gene expression varies in tobacco leaves subjected to treatments with different CO₂ concentrations (ranging from 0 to 800 ppm), inducing changes in photosynthesis, stomatal regulation and water evaporation from the leaf. Changes in air CO₂ concentration ([CO₂]) affected net photosynthesis (Pn) and leaf substomatal [CO₂] (Ci). Pn was slightly negative at 0 ppm air CO₂; it was one-third that of ambient controls at 200 ppm, and not different from controls at 800 ppm. Leaves fed with 800 ppm [CO₂] showed one-third reduced stomatal conductance (gs) and transpiration (E), and their gs was in turn slightly lower than in 200 ppm- and in 0 ppm-treated leaves. The 800 ppm air [CO₂] strongly impaired both NtAQP1 and NtPIP2;1 gene expression, whereas 0 ppm air [CO₂], a concentration below any in vivo possible conditions and specifically chosen to maximize the gene expression alteration, increased only the NtAQP1 transcript level. We propose that NtAQP1 expression, an aquaporin devoted to CO₂ transport, positively responds to CO₂ scarcity in the air in the whole range 0-800 ppm. On the contrary, expression of NtPIP2;1, an aquaporin not devoted to CO₂ transport, is related to water balance in the leaf, and changes in parallel with gs. These observations fit in a model where upregulation of leaf aquaporins is activated at low Ci, while downregulation occurs when high Ci saturates photosynthesis and causes stomatal closure.

Quantitative RT-PCR Platform to Measure Transcript Levels of C and N Metabolism-Related Genes in Durum Wheat: Transcript Profiles in Elevated [CO2] and High Temperature at Different Levels of N Supply

Only limited public transcriptomics resources are available for durum wheat and its responses to environmental changes. We developed a quantitative reverse transcription-PCR (qRT-PCR) platform for analysing the expression of primary C and N metabolism genes in durum wheat in leaves (125 genes) and roots (38 genes), based on available bread wheat genes and the identification of orthologs of known genes in other species. We also assessed the expression stability of seven reference genes for qRT-PCR under varying environments. We therefore present a functional qRT-PCR platform for gene expression analysis in durum wheat, and suggest using the ADP-ribosylation factor as a reference gene for qRT-PCR normalization. We investigated the effects of elevated [CO(2)] and temperature at two levels of N supply on C and N metabolism by combining gene expression analysis, using our qRT-PCR platform, with biochemical and physiological parameters in durum wheat grown in field chambers. Elevated CO(2) down-regulated the photosynthetic capacity and led to the loss of N compounds, including Rubisco; this effect was exacerbated at low N. Mechanistically, the reduction in photosynthesis and N levels could be associated with a decreased transcription of the genes involved in photosynthesis and N assimilation. High temperatures increased stomatal conductance, and thus did not inhibit photosynthesis, even though Rubisco protein and activity, soluble protein, leaf N, and gene expression for C fixation and N assimilation were down-regulated. Under a future scenario of climate change, the extent to which C fixation capacity and N assimilation are down-regulated will depend upon the N supply.

Expression patterns of C- and N-metabolism related genes in wheat are changed during senescence under elevated CO2 in dry-land agriculture

Projected climatic impacts on crop yield and quality, and increased demands for production, require targeted research to optimise nutrition of crop plants. For wheat, post-anthesis carbon and nitrogen remobilisation from vegetative plant parts and translocation to grains directly affects grain carbon (C), nitrogen (N) and protein levels. We analysed the influence of increased atmospheric CO2 on the expression of genes involved in senescence, leaf carbohydrate and nitrogen metabolism and assimilate transport in wheat under field conditions (Australian Grains Free Air CO2 Enrichment; AGFACE) over a time course from anthesis to maturity, the key period for grain filling. Wheat grown under CO2 enrichment had lower N concentrations and a tendency towards greater C/N ratios. A general acceleration of the senescence process by elevated CO2 was not confirmed. The expression patterns of genes involved in carbohydrate metabolism, nitrate reduction and metabolite transport differed between CO2 treatments, and this CO2 effect was different between pre-senescence and during senescence. The results suggest up-regulation of N remobilisation and down-regulation of C remobilisation during senescence under elevated CO2, which is consistent with greater grain N-sink strength of developing grains.

Expression of major photosynthetic and salt-resistance genes in invasive reed lineages grown under elevated CO2 and temperature

It is important to investigate the molecular causes of the variation in ecologically important traits to fully understand phenotypic responses to climate change. In the Mississippi River Delta, two distinct, sympatric invasive lineages of common reed (Phragmites australis) are known to differ in several ecophysiological characteristics and are expected to become more salt resistant due to increasing atmospheric CO2 and temperature. We investigated whether different patterns of gene expression can explain their ecophysiological differences and increased vigor under future climatic conditions. We compared the transcript abundance of photosynthetic genes of the Calvin cycle (Rubisco small subunit, RbcS; Phosphoglycerate kinase, PGK; Phosphoribulokinase, PRK), genes related with salt transport (Na(+)/H(+) antiporter, PhaNHA) and oxidative stress response genes (Manganese Superoxide dismutase, MnSOD; Glutathione peroxidase, GPX), and the total aboveground biomass production between two genotypes representing the two lineages. The two genotypes (Delta-type, Mediterranean lineage, and EU-type, Eurasian lineage) were grown under an ambient and a future climate scenario with simultaneously elevated CO2 and temperature, and under two different soil salinities (0‰ or 20‰). We found neither differences in the aboveground biomass production nor the transcript abundances of the two genotypes, but soil salinity significantly affected all the investigated parameters, often interacting with the climatic conditions. At 20‰ salinity, most genes were higher expressed in the future than in the ambient climatic conditions. Higher transcription of the genes suggests higher abundance of the protein they code for, and consequently increased photosynthate production, improved stress responses, and salt exclusion. Therefore, the higher expression of these genes most likely contributed to the significantly ameliorated salinity impact on the aboveground biomass production of both P. australis genotypes under elevated temperature and CO2. Although transcript abundances did not explain differences between the lineages, they correlated with the increased vigor of both lineages under anticipated future climatic conditions.

Genes responsive to elevated CO2 concentrations in triploid white poplar and integrated gene network analysis

BACKGROUND

The atmospheric CO2 concentration increases every year. While the effects of elevated CO2 on plant growth, physiology and metabolism have been studied, there is now a pressing need to understand the molecular mechanisms of how plants will respond to future increases in CO2 concentration using genomic techniques.

PRINCIPAL FINDINGS

Gene expression in triploid white poplar ((Populus tomentosa ×P. bolleana) ×P. tomentosa) leaves was investigated using the Affymetrix poplar genome gene chip, after three months of growth in controlled environment chambers under three CO2 concentrations. Our physiological findings showed the growth, assessed as stem diameter, was significantly increased, and the net photosynthetic rate was decreased in elevated CO2 concentrations. The concentrations of four major endogenous hormones appeared to actively promote plant development. Leaf tissues under elevated CO2 concentrations had 5,127 genes with different expression patterns in comparison to leaves under the ambient CO2 concentration. Among these, 8 genes were finally selected for further investigation by using randomized variance model corrective ANOVA analysis, dynamic gene expression profiling, gene network construction, and quantitative real-time PCR validation. Among the 8 genes in the network, aldehyde dehydrogenase and pyruvate kinase were situated in the core and had interconnections with other genes.

CONCLUSIONS

Under elevated CO2 concentrations, 8 significantly changed key genes involved in metabolism and responding to stimulus of external environment were identified. These genes play crucial roles in the signal transduction network and show strong correlations with elevated CO2 exposure. This study provides several target genes, further investigation of which could provide an initial step for better understanding the molecular mechanisms of plant acclimation and evolution in future rising CO2 concentrations.

Transcriptional reprogramming and stimulation of leaf respiration by elevated CO2 concentration is diminished, but not eliminated, under limiting nitrogen supply

Plant respiration responses to elevated CO2 concentration ( [CO2 ] ) have been studied for three decades without consensus about the mechanism of response. Positive effects of elevated [CO2 ] on leaf respiration have been attributed to greater substrate supply resulting from stimulated photosynthesis. Negative effects of elevated [CO2 ] on leaf respiration have been attributed to reduced demand for energy for protein turnover assumed to result from lower leaf N content. Arabidopsis thaliana was grown in ambient (370 ppm) and elevated (750 ppm) [CO2 ] with limiting and ample N availabilities. The stimulation of leaf dark respiration was attenuated in limiting N (+12%) compared with ample N supply (+30%). This response was associated with smaller stimulation of photosynthetic CO2 uptake, but not interactive effects of elevated CO2 and N supply on leaf protein, amino acids or specific leaf area. Elevated [CO2 ] also resulted in greater abundance of transcripts for many components of the respiratory pathway. A greater transcriptional response to elevated [CO2 ] was observed in ample N supply at midday versus midnight, consistent with reports that protein synthesis is greatest during the day. Greater foliar expression of respiratory genes under elevated [CO2 ] has now been observed in diverse herbaceous species, suggesting a widely conserved response.

Elevated CO2 increases the abundance of the peach aphid on Arabidopsis by reducing jasmonic acid defenses

Rising atmospheric CO2 concentrations can affect the induced defense of plants against herbivory by chewing insects, but little is known about whether elevated CO2 can change the inducible defense of plants against herbivory by aphids, which are phloem-sucking rather than tissue-chewing insects. Interactions between the green peach aphid Myzus persicae and four isogenic Arabidopsis thaliana genotypes including wild type and three induced defense pathway deficient mutants were examined under ambient and elevated CO2. Our data showed that elevated CO2 increased the population abundance of peach aphid when reared on wild type and SA-deficient mutant plants. Regardless of aphid infestation, elevated CO2 decreased the jasmonic acid (JA) but increased the salicylic acid (SA) level in wild-type plants. In addition, elevated CO2 increased SA level in SA-deficient mutant while did not change the JA level in JA-deficient mutant. Pathway enrichment analysis based on high-throughput transcriptome sequencing suggested that CO2 level, aphid infestation, and their interactions (respectively) altered plant defense pathways. Furthermore, qPCR results showed that elevated CO2 up-regulated the expression of SA-dependent defense genes but down-regulated the expression of JA/ethylene-dependent defense genes in wild-type plants infested by aphids. The current study indicated that elevated CO2 tended to enhance the ineffective defense-SA signaling pathway and to reduce the effective defense-JA signaling pathway against aphids, which resulted in increased aphid numbers.

Global transcriptomic profiling of aspen trees under elevated [CO2] to identify potential molecular mechanisms responsible for enhanced radial growth

Aspen (Populus tremuloides) trees growing under elevated [CO(2)] at a free-air CO(2) enrichment (FACE) site produced significantly more biomass than control trees. We investigated the molecular mechanisms underlying the observed increase in biomass by producing transcriptomic profiles of the vascular cambium zone (VCZ) and leaves, and then performed a comparative study to identify significantly changed genes and pathways after 12 years exposure to elevated [CO(2)]. In leaves, elevated [CO(2)] enhanced expression of genes related to Calvin cycle activity and linked pathways. In the VCZ, the pathways involved in cell growth, cell division, hormone metabolism, and secondary cell wall formation were altered while auxin conjugation, ABA synthesis, and cytokinin glucosylation and degradation were inhibited. Similarly, the genes involved in hemicellulose and pectin biosynthesis were enhanced, but some genes that catalyze important steps in lignin biosynthesis pathway were inhibited. Evidence from systemic analysis supported the functioning of multiple molecular mechanisms that underpin the enhanced radial growth in response to elevated [CO(2)].

Transcriptional and metabolic insights into the differential physiological responses of arabidopsis to optimal and supraoptimal atmospheric CO2

BACKGROUND

In tightly closed human habitats such as space stations, locations near volcano vents and closed culture vessels, atmospheric CO(2) concentration may be 10 to 20 times greater than Earth's current ambient levels. It is known that super-elevated (SE) CO(2) (>1,200 µmol mol(-1)) induces physiological responses different from that of moderately elevated CO(2) (up to 1,200 µmol mol(-1)), but little is known about the molecular responses of plants to supra-optimal [CO(2)].

METHODOLOGY/PRINCIPAL FINDINGS

To understand the underlying molecular causes for differential physiological responses, metabolite and transcript profiles were analyzed in aerial tissue of Arabidopsis plants, which were grown under ambient atmospheric CO(2) (400 µmol mol(-1)), elevated CO(2) (1,200 µmol mol(-1)) and SE CO(2) (4,000 µmol mol(-1)), at two developmental stages early and late vegetative stage. Transcript and metabolite profiling revealed very different responses to elevated versus SE [CO(2)]. The transcript profiles of SE CO(2) treated plants were closer to that of the control. Development stage had a clear effect on plant molecular response to elevated and SE [CO(2)]. Photosynthetic acclimation in terms of down-regulation of photosynthetic gene expression was observed in response to elevated [CO(2)], but not that of SE [CO(2)] providing the first molecular evidence that there appears to be a fundamental disparity in the way plants respond to elevated and SE [CO(2)]. Although starch accumulation was induced by both elevated and SE [CO(2)], the increase was less at the late vegetative stage and accompanied by higher soluble sugar content suggesting an increased starch breakdown to meet sink strength resulting from the rapid growth demand. Furthermore, many of the elevated and SE CO(2)-responsive genes found in the present study are also regulated by plant hormone and stress.

CONCLUSIONS/SIGNIFICANCE

This study provides new insights into plant acclimation to elevated and SE [CO(2)] during development and how this relates to stress, sugar and hormone signaling.

Genome-wide patterns of Arabidopsis gene expression in nature

Organisms in the wild are subject to multiple, fluctuating environmental factors, and it is in complex natural environments that genetic regulatory networks actually function and evolve. We assessed genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis thaliana and examined the nature of transcriptional variation throughout its life cycle and gene expression correlations with natural environmental fluctuations. We grew plants in a natural field environment and measured genome-wide time-series gene expression from the plant shoot every three days, spanning the seedling to reproductive stages. We find that 15,352 genes were expressed in the A. thaliana shoot in the field, and accession and flowering status (vegetative versus flowering) were strong components of transcriptional variation in this plant. We identified between ∼110 and 190 time-varying gene expression clusters in the field, many of which were significantly overrepresented by genes regulated by abiotic and biotic environmental stresses. The two main principal components of vegetative shoot gene expression (PC(veg)) correlate to temperature and precipitation occurrence in the field. The largest PC(veg) axes included thermoregulatory genes while the second major PC(veg) was associated with precipitation and contained drought-responsive genes. By exposing A. thaliana to natural environments in an open field, we provide a framework for further understanding the genetic networks that are deployed in natural environments, and we connect plant molecular genetics in the laboratory to plant organismal ecology in the wild.

Photosynthetic control of electron transport and the regulation of gene expression

The term 'photosynthetic control' describes the short- and long-term mechanisms that regulate reactions in the photosynthetic electron transport (PET) chain so that the rate of production of ATP and NADPH is coordinated with the rate of their utilization in metabolism. At low irradiances these mechanisms serve to optimize light use efficiency, while at high irradiances they operate to dissipate excess excitation energy as heat. Similarly, the production of ATP and NADPH in ratios tailored to meet demand is finely tuned by a sophisticated series of controls that prevents the accumulation of high NAD(P)H/NAD(P) ratios and ATP/ADP ratios that would lead to potentially harmful over-reduction and inactivation of PET chain components. In recent years, photosynthetic control has also been extrapolated to the regulation of gene expression because mechanisms that are identical or similar to those that serve to regulate electron flow through the PET chain also coordinate the regulated expression of genes encoding photosynthetic proteins. This requires coordinated gene expression in the chloroplasts, mitochondria, and nuclei, involving complex networks of forward and retrograde signalling pathways. Photosynthetic control operates to control photosynthetic gene expression in response to environmental and metabolic changes. Mining literature data on transcriptome profiles of C(3) and C(4) leaves from plants grown under high atmospheric carbon dioxide (CO(2)) levels compared with those grown with ambient CO(2) reveals that the transition to higher photorespiratory conditions in C(3) plants enhances the expression of genes associated with cyclic electron flow pathways in Arabidopsis thaliana, consistent with the higher ATP requirement (relative to NADPH) of photorespiration.

Greater antioxidant and respiratory metabolism in field-grown soybean exposed to elevated O3 under both ambient and elevated CO2

Antioxidant metabolism is responsive to environmental conditions, and is proposed to be a key component of ozone (O(3)) tolerance in plants. Tropospheric O(3) concentration ([O(3)]) has doubled since the Industrial Revolution and will increase further if precursor emissions rise as expected over this century. Additionally, atmospheric CO(2) concentration ([CO(2)]) is increasing at an unprecedented rate and will surpass 550 ppm by 2050. This study investigated the molecular, biochemical and physiological changes in soybean exposed to elevated [O(3) ] in a background of ambient [CO(2)] and elevated [CO(2)] in the field. Previously, it has been difficult to demonstrate any link between antioxidant defences and O(3) stress under field conditions. However, this study used principle components analysis to separate variability in [O(3)] from variability in other environmental conditions (temperature, light and relative humidity). Subsequent analysis of covariance determined that soybean antioxidant metabolism increased with increasing [O(3)], in both ambient and elevated [CO(2)]. The transcriptional response was dampened at elevated [CO(2)], consistent with lower stomatal conductance and lower O(3) flux into leaves. Energetically expensive increases in antioxidant metabolism and tetrapyrrole synthesis at elevated [O(3)] were associated with greater transcript levels of enzymes involved in respiratory metabolism.

Transcriptome analyses of Populus x euramericana clone I-214 leaves exposed to excess zinc

Zinc (Zn) is an essential element for plant growth and development, but at high levels this metal can become toxic. Hyperaccumulator species are often not suitable for phytoremediation technologies because they need to be fast growing and have high biomass production, such as those of the Populus genus. Comparative genomics studies of poplars subjected to stress conditions such as heavy metal contamination have generated resources useful for improving the annotation of genes and have provided novel insights in the defense/tolerance mechanisms governing adaptation in non-hyperaccumulator plants. Using a microarray-based comparative analysis, we identified functional gene sets that are differentially regulated in the leaves of Populus × euramericana clone I-214 subjected to an excess but sub-lethal dose of Zn (1 mM). Eco-physiological and chemical analyses confirmed the results obtained in previous similar experiments. A total of 3861 expressed sequence tags (ESTs) were differentially expressed and grouped into two distinct libraries of up-regulated (40%) and down-regulated (60%) putative genes. The annotation of genes and gene products according to the Gene Ontology vocabularies was performed using Blast2GO software. The two transcriptome data sets were used to query all known Kyoto Encyclopedia of Genes and Genomes (KEGG) biosynthetic pathways of the genes identified in this study. The most represented molecular functions and biological processes were nucleotide binding and transcription, transport and response to stress and abiotic and biotic stimuli. The chloroplast, mitochondrion and their membrane systems were the cellular components most affected by excess Zn, as well as the photosynthetic, defense, sulfur and glutathione (GSH) metabolic pathways. The most up-regulated genes encoded electron carriers associated with ferrodoxin, the small subunit of ribulose-bisphosphate carboxylase oxygenase, and enzymes involved in GSH metabolism. This study is the most in-depth transcriptome and gene-annotation analysis of a hybrid poplar to date. The results are presented and critically discussed in terms of poplar response/tolerance to Zn stress for the characterization of non-hyperaccumulator phenotypes and the identification of candidate genes in perennial plants. These genetic findings provide useful information on tree species' adaptation to metal stress and provide powerful tools for the selection and/or genetic manipulation of stress-tolerant poplar clones.

Vertical profiles reveal impact of ozone and temperature on carbon assimilation of Betula pendula and Populus tremula

Rising temperature and tropospheric ozone (O(3)) concentrations are likely to affect carbon assimilation processes and thus the carbon sink strength of trees. In this study, we investigated the joint action of elevated ozone and temperature on silver birch (Betula pendula) and European aspen (Populus tremula) saplings in field conditions by combining free-air ozone exposure (1.2 × ambient) and infrared heaters (ambient +1.2&emsp14;°C). At leaf level measurements, elevated ozone decreased leaf net photosynthesis (P(n)), while the response to elevated temperature was dependent on leaf position within the foliage. This indicates that leaf position has to be taken into account when leaf level data are collected and applied. The ozone effect on P(n) was partly compensated for at elevated temperature, showing an interactive effect of the treatments. In addition, the ratio of photosynthesis to stomatal conductance (P(n)/g(s) ratio) was decreased by ozone, which suggests decreasing water use efficiency. At the plant level, the increasing leaf area at elevated temperature resulted in a considerable increase in photosynthesis and growth in both species.

Forest tree genomics: growing resources and applications

Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.

Living with high putrescine: expression of ornithine and arginine biosynthetic pathway genes in high and low putrescine producing poplar cells

Arginine (Arg) and ornithine (Orn), both derived from glutamate (Glu), are the primary substrates for polyamine (PA) biosynthesis, and also play important roles as substrates and intermediates of overall N metabolism in plants. Their cellular homeostasis is subject to multiple levels of regulation. Using reverse transcription quantitative PCR (RT-qPCR), we studied changes in the expression of all genes of the Orn/Arg biosynthetic pathway in response to up-regulation [via transgenic expression of mouse Orn decarboxylase (mODC)] of PA biosynthesis in poplar (Populus nigra × maximowiczii) cells grown in culture. Cloning and sequencing of poplar genes involved in the Orn/Arg biosynthetic pathway showed that they have high homology with similar genes in other plants. The expression of the genes of Orn, Arg and PA biosynthetic pathway fell into two hierarchical clusters; expression of one did not change in response to high putrescine, while members of the other cluster showed a shift in expression pattern during the 7-day culture cycle. Gene expression of branch point enzymes (N-acetyl-Glu synthase, Orn aminotransferase, Arg decarboxylase, and spermidine synthase) in the sub-pathways, constituted a separate cluster from those involved in intermediary reactions of the pathway (N-acetyl-Glu kinase, N-acetyl-Glu-5-P reductase, N-acetyl-Orn aminotransferase, N (2)-acetylOrn:N-acetyl-Glu acetyltransferase, N (2)-acetyl-Orn deacetylase, Orn transcarbamylase, argininosuccinate synthase, carbamoylphosphate synthetase, argininosuccinate lyase, S-adenosylmethionine decarboxylase, spermine synthase). We postulate that expression of all genes of the Glu-Orn-Arg pathway is constitutively coordinated and is not influenced by the increase in flux rate through this pathway in response to increased utilization of Orn by mODC; thus the pathway involves mostly biochemical regulation rather than changes in gene expression. We further suggest that Orn itself plays a major role in the regulation of this pathway.

Differential gene expression in senescing leaves of two silver birch genotypes in response to elevated CO2 and tropospheric ozone

Long-term effects of elevated CO(2) and O(3) concentrations on gene expression in silver birch (Betula pendula Roth) leaves were studied during the end of the growing season. Two birch genotypes, clones 4 and 80, with different ozone growth responses, were exposed to 2x ambient CO(2) and/or O(3) in open-top chambers (OTCs). Microarray analyses were performed after 2 years of exposure, and the transcriptional profiles were compared to key physiological characteristics during leaf senescence. There were genotypic differences in the responses to CO(2) and O(3). Clone 80 exhibited greater transcriptional response and capacity to alter metabolism, resulting in better stress tolerance. The gene expression patterns of birch leaves indicated contrasting responses of senescence-related genes to elevated CO(2) and O(3). Elevated CO(2) delayed leaf senescence and reduced associated transcriptional changes, whereas elevated O(3) advanced leaf senescence because of increased oxidative stress. The combined treatment demonstrated that elevated CO(2) only temporarily alleviated the negative effects of O(3). Gene expression data alone were insufficient to explain the O(3) response in birch, and additional physiological and biochemical data were required to understand the true O(3) sensitivity of these clones.

The transcriptome of Populus in elevated CO reveals increased anthocyanin biosynthesis during delayed autumnal senescence

*The delay in autumnal senescence that has occurred in recent decades has been linked to rising temperatures. Here, we suggest that increasing atmospheric CO2 may partly account for delayed autumnal senescence and for the first time, through transcriptome analysis, identify gene expression changes associated with this delay. *Using a plantation of Populus x euramericana grown in elevated [CO2] (e[CO2]) with free-air CO2 enrichment (FACE) technology, we investigated the molecular and biochemical basis of this response. A Populus cDNA microarray was used to identify genes representing multiple biochemical pathways influenced by e[CO2] during senescence. Gene expression changes were confirmed through real-time quantitative PCR, and leaf biochemical assays. *Pathways for secondary metabolism and glycolysis were significantly up-regulated by e[CO2] during senescence, in particular, those related to anthocyanin biosynthesis. Expressed sequence tags (ESTs) representing the two most significantly up-regulated transcripts in e[CO2], LDOX (leucoanthocyanidin dioxgenase) and DFR (dihydroflavonol reductase), gave (e[CO2]/ambient CO(2) (a[CO2])) expression ratios of 39.6 and 19.3, respectively. *We showed that in e[CO2] there was increased autumnal leaf sugar accumulation and up-regulation of genes determining anthocyanin biosynthesis which, we propose, prolongs leaf longevity during natural autumnal senescence.

Gene expression responses of paper birch (Betula papyrifera) to elevated CO2 and O3 during leaf maturation and senescence

Gene expression responses of paper birch (Betula papyrifera) leaves to elevated concentrations of CO(2) and O(3) were studied with microarray analyses from three time points during the summer of 2004 at Aspen FACE. Microarray data were analyzed with clustering techniques, self-organizing maps, K-means clustering and Sammon's mappings, to detect similar gene expression patterns within sampling times and treatments. Most of the alterations in gene expression were caused by O(3), alone or in combination with CO(2). O(3) induced defensive reactions to oxidative stress and earlier leaf senescence, seen as decreased expression of photosynthesis- and carbon fixation-related genes, and increased expression of senescence-associated genes. The effects of elevated CO(2) reflected surplus of carbon that was directed to synthesis of secondary compounds. The combined CO(2)+O(3) treatment resulted in differential gene expression than with individual gas treatments or in changes similar to O(3) treatment, indicating that CO(2) cannot totally alleviate the harmful effects of O(3).

Transcriptomic comparison in the leaves of two aspen genotypes having similar carbon assimilation rates but different partitioning patterns under elevated [CO2]

This study compared the leaf transcription profiles, physiological characteristics and primary metabolites of two Populus tremuloides genotypes (clones 216 and 271) known to differ in their responses to long-term elevated [CO2] (e[CO2]) at the Aspen free-air CO2 enrichment site near Rhinelander, WI, USA. The physiological responses of these clones were similar in terms of photosynthesis, stomatal conductance and leaf area index under e[CO2], yet very different in terms of growth enhancement (0-10% in clone 216; 40-50% in clone 271). Although few genes responded to long-term exposure to e[CO2], the transcriptional activity of leaf e[CO2]-responsive genes was distinctly different between the clones, differentially impacting multiple pathways during both early and late growing seasons. An analysis of transcript abundance and carbon/nitrogen biochemistry suggested that the CO2-responsive clone (271) partitions carbon into pathways associated with active defense/response to stress, carbohydrate/starch biosynthesis and subsequent growth. The CO2-unresponsive clone (216) partitions carbon into pathways associated with passive defense (e.g. lignin, phenylpropanoid) and cell wall thickening. This study indicates that there is significant variation in expression patterns between different tree genotypes in response to long-term exposure to e[CO2]. Consequently, future efforts to improve productivity or other advantageous traits for carbon sequestration should include an examination of genetic variability in CO2 responsiveness.

Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants

BACKGROUND

Arabidopsis ovules comprise four morphologically distinct parts: the nucellus, which contains the embryo sac, two integuments that become the seed coat, and the funiculus that anchors the ovule within the carpel. Analysis of developmental mutants has shown that ovule morphogenesis relies on tightly regulated genetic interactions that can serve as a model for developmental regulation. Redundancy, pleiotropic effects and subtle phenotypes may preclude identification of mutants affecting some processes in screens for phenotypic changes. Expression-based gene discovery can be used access such obscured genes.

RESULTS

Affymetrix microarrays were used for expression-based gene discovery to identify sets of genes expressed in either or both integuments. The genes were identified by comparison of pistil mRNA from wild type with mRNA from two mutants; inner no outer (ino, which lacks the outer integument), and aintegumenta (ant, which lacks both integuments). Pools of pistils representing early and late stages of ovule development were evaluated and data from the three genotypes were used to designate genes that were predominantly expressed in the integuments using pair-wise and cluster analyses. Approximately two hundred genes were found to have a high probability of preferential expression in these structures, and the predictive nature of the expression classes was confirmed with reverse transcriptase polymerase chain reaction and in situ hybridization.

CONCLUSION

The results showed that it was possible to use a mutant, ant, with broad effects on plant phenotype to identify genes expressed specifically in ovules, when coupled with predictions from known gene expression patterns, or in combination with a more specific mutant, ino. Robust microarray averaging (RMA) analysis of array data provided the most reliable comparisons, especially for weakly expressed genes. The studies yielded an over-abundance of transcriptional regulators in the identified genes, and these form a set of candidate genes for evaluation of roles in ovule development using reverse genetics.

Coppicing shifts CO2 stimulation of poplar productivity to above-ground pools: a synthesis of leaf to stand level results from the POP/EUROFACE experiment

A poplar short rotation coppice (SRC) grown for the production of bioenergy can combine carbon (C) storage with fossil fuel substitution. Here, we summarize the responses of a poplar (Populus) plantation to 6 yr of free air CO(2) enrichment (POP/EUROFACE consisting of two rotation cycles). We show that a poplar plantation growing in nonlimiting light, nutrient and water conditions will significantly increase its productivity in elevated CO(2) concentrations ([CO(2)]). Increased biomass yield resulted from an early growth enhancement and photosynthesis did not acclimate to elevated [CO(2)]. Sufficient nutrient availability, increased nitrogen use efficiency (NUE) and the large sink capacity of poplars contributed to the sustained increase in C uptake over 6 yr. Additional C taken up in high [CO(2)] was mainly invested into woody biomass pools. Coppicing increased yield by 66% and partly shifted the extra C uptake in elevated [CO(2)] to above-ground pools, as fine root biomass declined and its [CO(2)] stimulation disappeared. Mineral soil C increased equally in ambient and elevated [CO(2)] during the 6 yr experiment. However, elevated [CO(2)] increased the stabilization of C in the mineral soil. Increased productivity of a poplar SRC in elevated [CO(2)] may allow shorter rotation cycles, enhancing the viability of SRC for biofuel production.

A cross-species transcriptomics approach to identify genes involved in leaf development

BACKGROUND

We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.

RESULTS

Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.

CONCLUSION

This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.

A cross-species transcriptomics approach to identify genes involved in leaf development

BACKGROUND

We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.

RESULTS

Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.

CONCLUSION

This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.

Arabidopsis transcript and metabolite profiles: ecotype-specific responses to open-air elevated [CO2]

A Free-Air CO(2) Enrichment (FACE) experiment compared the physiological parameters, transcript and metabolite profiles of Arabidopsis thaliana Columbia-0 (Col-0) and Cape Verde Island (Cvi-0) at ambient (approximately 0.375 mg g(-1)) and elevated (approximately 0.550 mg g(-1)) CO(2) ([CO(2)]). Photoassimilate pool sizes were enhanced in high [CO(2)] in an ecotype-specific manner. Short-term growth at elevated [CO(2)] stimulated carbon gain irrespective of down-regulation of plastid functions and altered expression of genes involved in nitrogen metabolism resembling patterns observed under N-deficiency. The study confirmed well-known characteristics, but the use of a time course, ecotypic genetic differences, metabolite analysis and the focus on clusters of functional categories provided new aspects about responses to elevated [CO(2)]. Longer-term Cvi-0 responded by down-regulating functions favouring carbon accumulation, and both ecotypes showed altered expression of genes for defence, redox control, transport, signalling, transcription and chromatin remodelling. Overall, carbon fixation with a smaller commitment of resources in elevated [CO(2)] appeared beneficial, with the extra C only partially utilized possibly due to disturbance of the C : N ratio. To different degrees, both ecotypes perceived elevated [CO(2)] as a metabolic perturbation that necessitated increased functions consuming or storing photoassimilate, with Cvi-0 emerging as more capable of acclimating. Elevated [CO(2)] in Arabidopsis favoured adjustments in reactive oxygen species (ROS) homeostasis and signalling that defined genotypic markers.

Elevated CO2 increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane

Because of the economical relevance of sugarcane and its high potential as a source of biofuel, it is important to understand how this crop will respond to the foreseen increase in atmospheric [CO(2)]. The effects of increased [CO(2)] on photosynthesis, development and carbohydrate metabolism were studied in sugarcane (Saccharum ssp.). Plants were grown at ambient (approximately 370 ppm) and elevated (approximately 720 ppm) [CO(2)] during 50 weeks in open-top chambers. The plants grown under elevated CO(2) showed, at the end of such period, an increase of about 30% in photosynthesis and 17% in height, and accumulated 40% more biomass in comparison with the plants grown at ambient [CO(2)]. These plants also had lower stomatal conductance and transpiration rates (-37 and -32%, respectively), and higher water-use efficiency (c.a. 62%). cDNA microarray analyses revealed a differential expression of 35 genes on the leaves (14 repressed and 22 induced) by elevated CO(2). The latter are mainly related to photosynthesis and development. Industrial productivity analysis showed an increase of about 29% in sucrose content. These data suggest that sugarcane crops increase productivity in higher [CO(2)], and that this might be related, as previously observed for maize and sorghum, to transient drought stress.

Global expression profiling in leaves of free-growing aspen

BACKGROUND

Genomic studies are routinely performed on young plants in controlled environments which is very different from natural conditions. In reality plants in temperate countries are exposed to large fluctuations in environmental conditions, in the case of perennials over several years. We have studied gene expression in leaves of a free-growing aspen (Populus tremula) throughout multiple growing seasons

RESULTS

We show that gene expression during the first month of leaf development was largely determined by a developmental program although leaf expansion, chlorophyll accumulation and the speed of progression through this program was regulated by the temperature. We were also able to define "transcriptional signatures" for four different substages of leaf development. In mature leaves, weather factors were important for gene regulation.

CONCLUSION

This study shows that multivariate methods together with high throughput transcriptional methods in the field can provide additional, novel information as to plant status under changing environmental conditions that is impossible to mimic in laboratory conditions. We have generated a dataset that could be used to e.g. identify marker genes for certain developmental stages or treatments, as well as to assess natural variation in gene expression.

Ecologically relevant genetic variation from a non-Arabidopsis perspective

Ecologically relevant genetic variation occurs in genes harbouring alleles that are adaptive in some environments but not in others. Analysis of this type of genetic variation in model organisms has made substantial progress, and is now being expanded to other species in order to better cover the diversity of plant life. Recent advances in connecting ecological and molecular studies in non-model species have been made with regard to edaphic and climatic adaptation, plant reproduction, life-history parameters and biotic interactions. New research avenues that increase biological complexity and ecological relevance by integrating ecological experiments with population genetic and functional genomic approaches provide new insights into the genetic basis of ecologically relevant variation.

Transcriptional profiling reveals elevated CO2 and elevated O3 alter resistance of soybean (Glycine max) to Japanese beetles (Popillia japonica)

The accumulation of CO2 and O3 in the troposphere alters phytochemistry which in turn influences the interactions between plants and insects. Using microarray analysis of field-grown soybean (Glycine max), we found that the number of transcripts in the leaves affected by herbivory by Japanese beetles (Popillia japonica) was greater when plants were grown under elevated CO2, elevated O3 and the combination of elevated CO2 plus elevated O3 than when grown in ambient atmosphere. The effect of herbivory on transcription diminished strongly with time (<1% of genes were affected by herbivory after 3 weeks), and elevated CO2 interacted more strongly with herbivory than elevated O3. The majority of transcripts affected by elevated O3 were related to antioxidant metabolism. Constitutive levels and the induction by herbivory of key transcripts associated with defence and hormone signalling were down-regulated under elevated CO2; 1-aminocyclopropane-1-carboxylate (ACC) synthase, lipoxygenase (LOX), allene oxide synthase (AOS), allene oxide cyclase (AOC), chalcone synthase (CHS), polyphenol oxidase (PPO) and cysteine protease inhibitor (CystPI) were lower in abundance compared with levels under ambient conditions. By suppressing the ability to mount an effective defence, elevated CO2 may decrease resistance of soybean to herbivory.

Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants

Background

One of the eminent opportunities afforded by modern genomic technologies is the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotypic variation and the resultant appearance of distinct physiological traits. Indeed much progress has been made in this area, particularly in biomedicine where functional genomic information can be used to determine the physiological state (e.g., diagnosis) and predict phenotypic outcome (e.g., patient survival). Ecology currently lacks an analogous approach where genomic information can be used to diagnose the presence of a given physiological state (e.g., stress response) and then predict likely phenotypic outcomes (e.g., stress duration and tolerance, fitness).

Results

Here, we demonstrate that a compendium of genomic signatures can be used to classify the plant abiotic stress phenotype in Arabidopsis according to the architecture of the transcriptome, and then be linked with gene coexpression network analysis to determine the underlying genes governing the phenotypic response. Using this approach, we confirm the existence of known stress responsive pathways and marker genes, report a common abiotic stress responsive transcriptome and relate phenotypic classification to stress duration.

Conclusion

Linking genomic signatures to gene coexpression analysis provides a unique method of relating an observed plant phenotype to changes in gene expression that underlie that phenotype. Such information is critical to current and future investigations in plant biology and, in particular, to evolutionary ecology, where a mechanistic understanding of adaptive physiological responses to abiotic stress can provide researchers with a tool of great predictive value in understanding species and population level adaptation to climate change.

Downregulation of cinnamoyl-coenzyme A reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure

Cinnamoyl-CoA reductase (CCR) catalyzes the penultimate step in monolignol biosynthesis. We show that downregulation of CCR in transgenic poplar (Populus tremula x Populus alba) was associated with up to 50% reduced lignin content and an orange-brown, often patchy, coloration of the outer xylem. Thioacidolysis, nuclear magnetic resonance (NMR), immunocytochemistry of lignin epitopes, and oligolignol profiling indicated that lignin was relatively more reduced in syringyl than in guaiacyl units. The cohesion of the walls was affected, particularly at sites that are generally richer in syringyl units in wild-type poplar. Ferulic acid was incorporated into the lignin via ether bonds, as evidenced independently by thioacidolysis and by NMR. A synthetic lignin incorporating ferulic acid had a red-brown coloration, suggesting that the xylem coloration was due to the presence of ferulic acid during lignification. Elevated ferulic acid levels were also observed in the form of esters. Transcript and metabolite profiling were used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers. Both methods suggested reduced biosynthesis and increased breakdown or remodeling of noncellulosic cell wall polymers, which was further supported by Fourier transform infrared spectroscopy and wet chemistry analysis. The reduced levels of lignin and hemicellulose were associated with an increased proportion of cellulose. Furthermore, the transcript and metabolite profiling data pointed toward a stress response induced by the altered cell wall structure. Finally, chemical pulping of wood derived from 5-year-old, field-grown transgenic lines revealed improved pulping characteristics, but growth was affected in all transgenic lines tested.

Mapping the proteome of poplar and application to the discovery of drought-stress responsive proteins

Poplar is the first forest tree genome to be decoded. As an initial step to the comprehensive analysis of poplar proteome, we described reference 2-D-maps for eight tissues/organs of the plant, and the functional characterization of some proteins. A total of 398 proteins were excised from the gels. About 91.2% were identified by nanospray LC-MS/MS, based on comparison with 260,000 Populus sp. ESTs. In comparison, reliable PMFs were obtained for only 51% of the spots by MALDI-TOF-MS, from which 43% (83 spots) positively matched gene models of the Populus trichocarpa genome sequence. Among these 83 spots, 58% matched with the same proteins as identified by LC-MS/MS, 21.7% with unknown function proteins and 19.3% with completely different functions. In the second phase, we studied the effect of drought stress on poplar root and leaf proteomes. The function of up- and down-regulated proteins is discussed with respect to the physiological response of the plants and compared with transcriptomic data. Some important clues regarding the way poplar copes with water deficit were revealed.