Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field

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.

The Complementary Roles of Chloroplast Cyclic Electron Transport and Mitochondrial Alternative Oxidase to Ensure Photosynthetic Performance

Chloroplasts use light energy and a linear electron transport (LET) pathway for the coupled generation of NADPH and ATP. It is widely accepted that the production ratio of ATP to NADPH is usually less than required to fulfill the energetic needs of the chloroplast. Left uncorrected, this would quickly result in an over-reduction of the stromal pyridine nucleotide pool (i.e., high NADPH/NADP⁺ ratio) and under-energization of the stromal adenine nucleotide pool (i.e., low ATP/ADP ratio). These imbalances could cause metabolic bottlenecks, as well as increased generation of damaging reactive oxygen species. Chloroplast cyclic electron transport (CET) and the chloroplast malate valve could each act to prevent stromal over-reduction, albeit in distinct ways. CET avoids the NADPH production associated with LET, while the malate valve consumes the NADPH associated with LET. CET could operate by one of two different pathways, depending upon the chloroplast ATP demand. The NADH dehydrogenase-like pathway yields a higher ATP return per electron flux than the pathway involving PROTON GRADIENT REGULATION5 (PGR5) and PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE1 (PGRL1). Similarly, the malate valve could couple with one of two different mitochondrial electron transport pathways, depending upon the cytosolic ATP demand. The cytochrome pathway yields a higher ATP return per electron flux than the alternative oxidase (AOX) pathway. In both Arabidopsis thaliana and Chlamydomonas reinhardtii, PGR5/PGRL1 pathway mutants have increased amounts of AOX, suggesting complementary roles for these two lesser-ATP yielding mechanisms of preventing stromal over-reduction. These two pathways may become most relevant under environmental stress conditions that lower the ATP demands for carbon fixation and carbohydrate export.

Nitrogen Systemic Signaling: From Symbiotic Nodulation to Root Acquisition

Plant nutrient acquisition is tightly regulated by resource availability and metabolic needs, implying the existence of communication between roots and shoots to ensure their integration at the whole-plant level. Here, we focus on systemic signaling pathways controlling nitrogen (N) nutrition, achieved both by the root import of mineral N and, in legume plants, through atmospheric N fixation by symbiotic bacteria inside dedicated root nodules. We explore features conserved between systemic pathways repressing or enhancing symbiotic N fixation and the regulation of mineral N acquisition by roots, as well as their integration with other environmental factors, such as phosphate, light, and CO₂ availability.

Distinctive mitochondrial and chloroplast components contributing to the maintenance of carbon balance during plant growth at elevated CO2

Plant carbon balance depends upon the difference between photosynthetic carbon gain and respiratory carbon loss. In C₃ plants, growth at an elevated atmospheric concentration of CO₂ (ECO₂) stimulates photosynthesis and raises the leaf carbohydrate status, but how respiration responds is less understood. In this study, growth of Nicotiana tabacum at ECO₂ increased the protein amount of the non-energy conserving mitochondrial alternative oxidase (AOX). Growth at ECO₂ increased AOX1a transcript amount, and the transcript amount of a putative sugar-responsive gene encoding a chloroplast glucose-6-phosphate/phosphate translocator (GPT3). We suggest that the elevated amounts of AOX and GPT3 represent distinctive mitochondrial and chloroplast mechanisms to manage an excessive cytosolic pool of sugar phosphates. AOX respiration could consume cytosolic sugar phosphates, without this activity being restricted by rates of ATP turnover. GPT3 could allow accumulating cytosolic glucose-6-phosphate to return to the chloroplast. This could feed starch synthesis or a glucose-6-phosphate shunt in the Calvin cycle. AOX and GPT3 activities could buffer against P_i depletions that might otherwise disrupt mitochondrial and chloroplast electron transport chain activities. AOX and GPT3 activities could also buffer against a down-regulation of photosynthetic capacity by preventing a persistent imbalance between photosynthetic carbon gain and the activity of carbon utilizing sinks.

Differential responses of photosynthetic parameters and its influence on carbohydrate metabolism in some contrasting rice (Oryza sativa L.) genotypes under arsenate stress

Influence of arsenic (As) in As tolerant and sensitive rice genotypes based chloroplastic pigments, leaf gas exchange attributes and their influence on carbohydrate metabolism were investigated in the present study. As retards growth of crop plants and increase several health ailments by contaminating food chain. Photosynthetic inhibition is known to be the prime target of As toxicity due to over-production of ROS. Hydroponically grown rice seedlings of twelve cultivars were exposed to 25, 50, and 75 μM arsenate (AsV) that exerted negative impact on plastidial pigments content and resulted into inhibition of Hill activity. Internal CO₂ concentration lowered gradually due to interference of As with stomatal conductance and transpiration rate that subsequently led to drop in net photosynthesis. Twelve contrasting rice genotypes responded differentially to As(V) stress. Present study evaluated As tolerant and sensitive rice cultivars with respect to As(V) imposed alterations in pigments content, photosynthetic attributes along with sugar metabolism. Starch contents, the principle carbohydrate storage declined differentially among As(V) stressed test cultivars, being more pronounced in cvs. Swarnadhan, Tulaipanji, Pusa basmati, Badshabhog, Tulsibhog and IR-20 compared to cvs. Bhutmuri, Kumargore, Binni, Vijaya, TN-1 and IR-64. Therefore, the six former cultivars tried to adapt defensive mechanisms by accumulating higher levels of reducing and non-reducing sugars to carry out basal metabolism to withstand As(V) induced alterations in photosynthesis. This study could help to screen As tolerant and sensitive rice genotypes based on their photosynthetic efficiency in As polluted agricultural fields to reduce As contamination assisted ecotoxicological risk.

CO2 Elevation Accelerates Phenology and Alters Carbon/Nitrogen Metabolism vis-à-vis ROS Abundance in Bread Wheat

Wheat is an important staple food crop of the world and it accounts for 18-20% of human dietary protein. Recent reports suggest that CO₂ elevation (CE) reduces grain protein and micronutrient content. In our earlier study, it was found that the enhanced production of nitric oxide (NO) and the concomitant decrease in transcript abundance as well as activity of nitrate reductase (NR) and high affinity nitrate transporters (HATS) resulted in CE-mediated decrease in N metabolites in wheat seedlings. In the current study, two bread wheat genotypes Gluyas Early and B.T. Schomburgk differing in nitrate uptake and assimilation properties were evaluated for their response to CE. To understand the impact of low (LN), optimal (ON) and high (HN) nitrogen supply on plant growth, phenology, N and C metabolism, ROS and RNS signaling and yield, plants were evaluated under short term (hydroponics experiment) and long term (pot experiment) CE. CE improved growth, altered N assimilation, C/N ratio, N use efficiency (NUE) in B.T. Schomburgk. In general, CE decreased shoot N concentration and grain protein concentration in wheat irrespective of N supply. CE accelerated phenology and resulted in early flowering of both the wheat genotypes. Plants grown under CE showed higher levels of nitrosothiol and ROS, mainly under optimal and high nitrogen supply. Photorespiratory ammonia assimilating genes were down regulated by CE, whereas, expression of nitrate transporter/NPF genes were differentially regulated between genotypes by CE under different N availability. The response to CE was dependent on N supply as well as genotype. Hence, N fertilizer recommendation needs to be revised based on these variables for improving plant responses to N fertilization under a future CE scenario.

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.

Short-term responses of soybean roots to individual and combinatorial effects of elevated [CO2] and water deficit

Climate change increasingly threatens plant growth and productivity. Soybean (Glycine max) is one of the most important crops in the world. Although its responses to increased atmospheric carbon dioxide concentration ([CO2]) have been previously studied, root molecular responses to elevated [CO2] (E[CO2]) or the combination/interaction of E[CO2] and water deficit remain unexamined. In this study, we evaluated the individual and combinatory effects of E[CO2] and water deficit on the physiology and root molecular responses in soybean. Plants growing under E[CO2] exhibited increased photosynthesis that resulted in a higher biomass, plant height, and leaf area. E[CO2] decreased the transcripts levels of genes involved in iron uptake and transport, antioxidant activity, secondary metabolism and defense, and stress responses in roots. When plants grown under E[CO2] are treated with instantaneous water deficit, E[CO2] reverted the expression of water deficit-induced genes related to stress, defense, transport and nutrient deficiency. Furthermore, the interaction of both treatments uniquely affected the expression of genes. Both physiological and transcriptomic analyses demonstrated that E[CO2] may mitigate the negative effects of water deficit on the soybean roots. In addition, the identification of genes that are modulated by the interaction of E[CO2] and water deficit suggests an emergent response that is triggered only under this specific condition.

Leaf-age dependent response of carotenoid accumulation to elevated CO2 in Arabidopsis

Carotenoids contribute to photosynthesis, photoprotection, phytohormone and apocarotenoid biosynthesis in plants. Carotenoid-derived metabolites control plant growth, development and signalling processes and their accumulation can depend upon changes in the environment. Elevated carbon dioxide (eCO₂) often enhances carbon assimilation, early growth patterns and overall plant biomass, and may increase carotenoid accumulation due to higher levels of precursors from isoprenoid biosynthesis. Variable effects of eCO₂ on carotenoid accumulation in leaves have been observed for different plant species. Here, we determined whether the variable response of carotenoids to eCO₂ was potentially a function of leaf age and the impact of eCO₂ on leaf development by growing Arabidopsis in ambient CO₂ (400 ppm) and eCO₂ (800 ppm). eCO₂ increased plant leaf number, rosette area, biomass, seed yield and net photosynthesis. In addition, eCO₂ increased carotenoid content by 10-20% in younger emerging leaves, but not in older mature leaves. Older leaves contained approximately 60% less total carotenoids compared to younger leaves. The age-dependent effect on carotenoid content was observed for cotyledon, juvenile and adult phase leaves. We conclude that younger leaves utilize additional carbon from enhanced photosynthesis in eCO₂ to increase carotenoid content, yet older leaves have less capacity to store additional carbon into carotenoids.

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.

Improved responses to elevated CO2 in durum wheat at a low nitrate supply associated with the upregulation of photosynthetic genes and the activation of nitrate assimilation

Elevated CO₂ often leads to photosynthetic acclimation, and N availability may alter this response. We investigated whether the coordination of shoot-root N assimilation by elevated CO₂ may help to optimize the whole-plant N allocation and maximize photosynthesis in hydroponically-grown durum wheat at two NO₃^- supplies in interaction with plant development. Transcriptional and biochemical analyses were performed on flag leaves and roots. At anthesis, the improved photosynthetic acclimation response to elevated CO₂ at low N was associated with increased Rubisco, chlorophyll and amino acid contents, and upregulation of genes related to their biosynthesis, light reactions and Calvin-Benson cycle, while a decrease was recorded at high N. Despite the decrease in carbohydrates with elevated CO₂ at low N and the increase at high N, a stronger upward trend in leaf NR activity was found at low rather than high N. The induction of N recycling-related genes was accompanied by an amino acids decline at high N. At the grain-filling stage, the photosynthetic acclimation to elevated CO₂ at high N was associated with the downregulation of both N assimilation, mainly in roots, and photosynthetic genes. At low N, enhanced root N assimilation partly compensated for slower shoot N assimilation and maximized photosynthetic capacity.

Atmospheric CO2 Alters Resistance of Arabidopsis to Pseudomonas syringae by Affecting Abscisic Acid Accumulation and Stomatal Responsiveness to Coronatine

Atmospheric CO2 influences plant growth and stomatal aperture. Effects of high or low CO2 levels on plant disease resistance are less well understood. Here, resistance of Arabidopsis thaliana against the foliar pathogen Pseudomonas syringae pv. tomato DC3000 (Pst) was investigated at three different CO2 levels: high (800 ppm), ambient (450 ppm), and low (150 ppm). Under all conditions tested, infection by Pst resulted in stomatal closure within 1 h after inoculation. However, subsequent stomatal reopening at 4 h, triggered by the virulence factor coronatine (COR), occurred only at ambient and high CO2, but not at low CO2. Moreover, infection by Pst was reduced at low CO2 to the same extent as infection by mutant Pst cor- . Under all CO2 conditions, the ABA mutants aba2-1 and abi1-1 were as resistant to Pst as wild-type plants under low CO2, which contained less ABA. Moreover, stomatal reopening mediated by COR was dependent on ABA. Our results suggest that reduced ABA levels at low CO2 contribute to the observed enhanced resistance to Pst by deregulation of virulence responses. This implies that enhanced ABA levels at increasing CO2 levels may have a role in weakening plant defense.

Metabolic and Transcriptional Analysis of Durum Wheat Responses to Elevated CO2 at Low and High Nitrate Supply

Elevated [CO₂] (eCO₂) can lead to photosynthetic acclimation and this is often intensified by low nitrogen (N). Despite intensive studies of plant responses to eCO₂, the regulation mechanism of primary metabolism at the whole-plant level in interaction with [Formula: see text] supply remains unclear. We examined the metabolic and transcriptional responses triggered by eCO₂ in association with physiological-biochemical traits in flag leaves and roots of durum wheat grown hydroponically in ambient and elevated [CO₂] with low (LN) and high (HN) [Formula: see text] supply. Multivariate analysis revealed a strong interaction between eCO₂ and [Formula: see text] supply. Photosynthetic acclimation induced by eCO₂ in LN plants was accompanied by an increase in biomass and carbohydrates, and decreases of leaf organic N per unit area, organic acids, inorganic ions, Calvin-Benson cycle intermediates, Rubisco, nitrate reductase activity, amino acids and transcripts for N metabolism, particularly in leaves, whereas [Formula: see text] uptake was unaffected. In HN plants, eCO₂ did not decrease photosynthetic capacity or leaf organic N per unit area, but induced transcripts for N metabolism, especially in roots. In conclusion, the photosynthetic acclimation in LN plants was associated with an inhibition of leaf [Formula: see text] assimilation, whereas up-regulation of N metabolism in roots could have mitigated the acclimatory effect of eCO₂ in HN plants.

Root-shoot interactions explain the reduction of leaf mineral content in Arabidopsis plants grown under elevated [CO2 ] conditions

Although shoot N depletion in plants exposed to elevated [CO2 ] has already been reported on several occasions, some uncertainty remains about the mechanisms involved. This study illustrates (1) the importance of characterizing root-shoot interactions and (2) the physiological, biochemical and gene expression mechanisms adopted by nitrate-fed Arabidopsis thaliana plants grown under elevated [CO2 ]. Elevated [CO2 ] increases biomass and photosynthetic rates; nevertheless, the decline in total soluble protein, Rubisco and leaf N concentrations revealed a general decrease in leaf N availability. A transcriptomic approach (conducted at the root and shoot level) revealed that exposure to 800 ppm [CO2 ] induced the expression of genes involved in the transport of nitrate and mineral elements. Leaf N and mineral status revealed that N assimilation into proteins was constrained under elevated [CO2 ]. Moreover, this study also highlights how elevated [CO2 ] induced the reorganization of nitrate assimilation between tissues; root nitrogen assimilation was favored over leaf assimilation to offset the decline in nitrogen metabolism in the leaves of plants exposed to elevated [CO2 ].

Effects of Elevated Atmospheric CO2 on Primary Metabolite Levels in Arabidopsis thaliana Col-0 Leaves: An Examination of Metabolome Data

Elevated atmospheric CO(2) concentrations ([CO(2)]) affect primary metabolite levels because CO(2) is a direct substrate for photosynthesis. In several studies, the responses of primary metabolite levels have been examined using Arabidopsis thaliana leaves, but these results have not been comprehensively discussed. Here, we examined metabolome data for A. thaliana accession Col-0 leaves that were grown at elevated [CO(2)] with sufficient nitrogen (N) nutrition. At elevated [CO(2)], starch, monosaccharides and several major amino acids accumulated in leaves. The degree of accumulation depended on whether the rooting medium contained NH(4) (+) or only NO(3) (-). Because low N conditions induce an increase in carbohydrates similar to that of elevated [CO(2)], we compared the responses of primary metabolite levels between elevated [CO(2)] and low N conditions. Levels of the tricarboxylic acid (TCA) cycle-associated organic acids and major amino acids decreased with low N, but not with elevated [CO(2)]. Even at elevated [CO(2)], the low N induced the decreases in the levels of organic acids and major amino acids. A small sink size also affects the primary metabolite response patterns in leaves under elevated [CO(2)] conditions. Thus, care is necessary when interpreting primary metabolite changes in leaves of field-grown plants.

Root and shoot performance of Arabidopsis thaliana exposed to elevated CO2: A physiologic, metabolic and transcriptomic response

The responsiveness of C3 plants to raised atmospheric [CO2] levels has been frequently described as constrained by photosynthetic downregulation. The main goal of the current study was to characterize the shoot-root relationship and its implications in plant responsiveness under elevated [CO2] conditions. For this purpose, Arabidopsis thaliana plants were exposed to elevated [CO2] (800ppm versus 400ppm [CO2]) and fertilized with a mixed (NH4NO3) nitrogen source. Plant growth, physiology, metabolite and transcriptomic characterizations were carried out at the root and shoot levels. Plant growth under elevated [CO2] conditions was doubled due to increased photosynthetic rates and gas exchange measurements revealed that these plants maintain higher photosynthetic rates over extended periods of time. This positive response of photosynthetic rates to elevated [CO2] was caused by the maintenance of leaf protein and Rubisco concentrations at control levels alongside enhanced energy efficiency. The increased levels of leaf carbohydrates, organic acids and amino acids supported the augmented respiration rates of plants under elevated [CO2]. A transcriptomic analysis allowed the identification of photoassimilate allocation and remobilization as fundamental process used by the plants to maintain the outstanding photosynthetic performance. Moreover, based on the relationship between plant carbon status and hormone functioning, the transcriptomic analyses provided an explanation of why phenology accelerates under elevated [CO2] conditions.

Response and adaptation of photosynthesis, respiration, and antioxidant systems to elevated CO2 with environmental stress in plants

It is well known that plant photosynthesis and respiration are two fundamental and crucial physiological processes, while the critical role of the antioxidant system in response to abiotic factors is still a focus point for investigating physiological stress. Although one key metabolic process and its response to climatic change have already been reported and reviewed, an integrative review, including several biological processes at multiple scales, has not been well reported. The current review will present a synthesis focusing on the underlying mechanisms in the responses to elevated CO2 at multiple scales, including molecular, cellular, biochemical, physiological, and individual aspects, particularly, for these biological processes under elevated CO2 with other key abiotic stresses, such as heat, drought, and ozone pollution, as well as nitrogen limitation. The present comprehensive review may add timely and substantial information about the topic in recent studies, while it presents what has been well established in previous reviews. First, an outline of the critical biological processes, and an overview of their roles in environmental regulation, is presented. Second, the research advances with regard to the individual subtopics are reviewed, including the response and adaptation of the photosynthetic capacity, respiration, and antioxidant system to CO2 enrichment alone, and its combination with other climatic change factors. Finally, the potential applications for plant responses at various levels to climate change are discussed. The above issue is currently of crucial concern worldwide, and this review may help in a better understanding of how plants deal with elevated CO2 using other mainstream abiotic factors, including molecular, cellular, biochemical, physiological, and whole individual processes, and the better management of the ecological environment, climate change, and sustainable development.

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.

Plant metabolite profiles and the buffering capacities of ecosystems

In spite of some inherent challenges, metabolite profiling is becoming increasingly popular under field conditions. It has been used successfully to address topics like species interactions, connections between growth and chemical stoichiometry or the plant's stress response. Stress exerts a particularly clear impact on plant metabolomes and has become a central topic in many metabolite profiling experiments in the fields. In contrast to phytochambers, however, external stress is often at least partially absorbed by the environment when measuring under field conditions. Such stress-buffering capacities of (agro)-ecosystems are of crucial interest given the ever-increasing anthropogenic impact on ecosystems and this review promotes the idea of using plant metabolite profiles for respective measurements. More specifically I propose to use parameters of the response of key plant species to a given stress treatment as proxies for measuring and comparing stress-buffering capacities of ecosystems. Stress response parameters accessible by metabolite profiling comprise for example the intensity or duration of the impact of stress or the ability of the plant organism to recover from this impact after a given time. Analyses of ecosystem stress-buffering capacities may improve our understanding of how ecosystems cope with stress and may improve our abilities to predict ecosystem changes.

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.

Linking gene expression and membrane lipid composition of Arabidopsis

Glycerolipid metabolism of plants responds dynamically to changes in light intensity and temperature, leading to the modification of membrane lipid composition to ensure optimal biochemical and physical properties in the new environment. Although multiple posttranscriptional regulatory mechanisms have been reported to be involved in the process, the contribution of transcriptional regulation remains largely unknown. Here, we present an integrative analysis of transcriptomic and lipidomic data, revealing large-scale coordination between gene expression and changes in glycerolipid levels during the Arabidopsis thaliana response to light and temperature stimuli. Using a multivariate regression technique called O2PLS, we show that the gene expression response is strictly coordinated at the biochemical pathway level and occurs in parallel with changes of specific glycerolipid pools. Five interesting candidate genes were chosen for further analysis from a larger set of candidates identified based on their close association with various groups of glycerolipids. Lipidomic analysis of knockout mutant lines of these five genes showed a significant relationship between the coordination of transcripts and glycerolipid levels in a changing environment and the effects of single gene perturbations.

Effects of elevated CO2 on levels of primary metabolites and transcripts of genes encoding respiratory enzymes and their diurnal patterns in Arabidopsis thaliana: possible relationships with respiratory rates

Elevated CO2 affects plant growth and photosynthesis, which results in changes in plant respiration. However, the mechanisms underlying the responses of plant respiration to elevated CO2 are poorly understood. In this study, we measured diurnal changes in the transcript levels of genes encoding respiratory enzymes, the maximal activities of the enzymes and primary metabolite levels in shoots of Arabidopsis thaliana grown under moderate or elevated CO2 conditions (390 or 780 parts per million by volume CO2, respectively). We examined the relationships between these changes and respiratory rates. Under elevated CO2, the transcript levels of several genes encoding respiratory enzymes increased at the end of the light period, but these increases did not result in changes in the maximal activities of the corresponding enzymes. The levels of some primary metabolites such as starch and sugar phosphates increased under elevated CO2, particularly at the end of the light period. The O2 uptake rate at the end of the dark period was higher under elevated CO2 than under moderate CO2, but higher under moderate CO2 than under elevated CO2 at the end of the light period. These results indicate that the changes in O2 uptake rates are not directly related to changes in maximal enzyme activities and primary metabolite levels. Instead, elevated CO2 may affect anabolic processes that consume respiratory ATP, thereby affecting O2 uptake rates.

The peptide-encoding CEP1 gene modulates lateral root and nodule numbers in Medicago truncatula

The role of MtCEP1, a member of the CEP (C-terminally encoded peptide) signaling peptide family, was examined in Medicago truncatula root development. MtCEP1 was expressed in root tips, vascular tissue, and young lateral organs, and was up-regulated by low nitrogen levels and, independently, by elevated CO2. Overexpressing MtCEP1 or applying MtCEP1 peptide to roots elicited developmental phenotypes: inhibition of lateral root formation, enhancement of nodulation, and the induction of periodic circumferential root swellings, which arose from cortical, epidermal, and pericycle cell divisions and featured an additional cortical cell layer. MtCEP peptide addition to other legume species induced similar phenotypes. The enhancement of nodulation by MtCEP1 is partially tolerant to high nitrate, which normally strongly suppresses nodulation. These nodules develop faster, are larger, and fix more nitrogen in the absence and presence of inhibiting nitrate levels. At 25mM nitrate, nodules formed on pre-existing swelling sites induced by MtCEP1 overexpression. RNA interference-mediated silencing of several MtCEP genes revealed a negative correlation between transcript levels of MtCEP1 and MtCEP2 with the number of lateral roots. MtCEP1 peptide-dependent phenotypes were abolished or attenuated by altering or deleting key residues in its 15 amino acid domain. RNA-Seq analysis revealed that 89 and 116 genes were significantly up- and down-regulated, respectively, by MtCEP1 overexpression, including transcription factors WRKY, bZIP, ERF, and MYB, homologues of LOB29, SUPERROOT2, and BABY BOOM. Taken together, the data suggest that the MtCEP1 peptide modulates lateral root and nodule development in M. truncatula.

CEP genes regulate root and shoot development in response to environmental cues and are specific to seed plants

The manifestation of repetitive developmental programmes during plant growth can be adjusted in response to various environmental cues. During root development, this means being able to precisely control root growth and lateral root development. Small signalling peptides have been found to play roles in many aspects of root development. One member of the CEP (C-TERMINALLY ENCODED PEPTIDE) gene family has been shown to arrest root growth. Here we report that CEP genes are widespread among seed plants but are not present in land plants that lack true branching roots or root vasculature. We have identified 10 additional CEP genes in Arabidopsis. Expression analysis revealed that CEP genes are regulated by environmental cues such as nitrogen limitation, increased salt levels, increased osmotic strength, and increased CO2 levels in both roots and shoots. Analysis of synthetic CEP variants showed that both peptide sequence and modifications of key amino acids affect CEP biological activity. Analysis of several CEP over-expression lines revealed distinct roles for CEP genes in root and shoot development. A cep3 knockout mutant showed increased root and shoot growth under a range of abiotic stress, nutrient, and light conditions. We demonstrate that CEPs are negative regulators of root development, slowing primary root growth and reducing lateral root formation. We propose that CEPs are negative regulators that mediate environmental influences on plant development.

A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis

Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H(+)-coupled K(+) transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells.

Action of gibberellins on growth and metabolism of Arabidopsis plants associated with high concentration of carbon dioxide

Although the positive effect of elevated CO(2) concentration [CO(2)] on plant growth is well known, it remains unclear whether global climate change will positively or negatively affect crop yields. In particular, relatively little is known about the role of hormone pathways in controlling the growth responses to elevated [CO(2)]. Here, we studied the impact of elevated [CO(2)] on plant biomass and metabolism in Arabidopsis (Arabidopsis thaliana) in relation to the availability of gibberellins (GAs). Inhibition of growth by the GA biosynthesis inhibitor paclobutrazol (PAC) at ambient [CO(2)] (350 µmol CO(2) mol(-1)) was reverted by elevated [CO(2)] (750 µmol CO(2) mol(-1)). Thus, we investigated the metabolic adjustment and modulation of gene expression in response to changes in growth of plants imposed by varying the GA regime in ambient and elevated [CO(2)]. In the presence of PAC (low-GA regime), the activities of enzymes involved in photosynthesis and inorganic nitrogen assimilation were markedly increased at elevated [CO(2)], whereas the activities of enzymes of organic acid metabolism were decreased. Under ambient [CO(2)], nitrate, amino acids, and protein accumulated upon PAC treatment; however, this was not the case when plants were grown at elevated [CO(2)]. These results suggest that only under ambient [CO(2)] is GA required for the integration of carbohydrate and nitrogen metabolism underlying optimal biomass determination. Our results have implications concerning the action of the Green Revolution genes in future environmental conditions.

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.

Multi-dimensional regulation of metabolic networks shaping plant development and performance

The metabolome is an integral part of a plant's life cycle and determines for a large part its external phenotype. It is the final, internal product of chemical interactions, obtained through developmental, genetic, and environmental inputs, and as such, it defines the state of a plant in terms of development and performance. Understanding its regulation will provide knowledge and new insights into the biochemical pathways and genetic interactions that shape the plant and its surroundings. In this review, we will focus on four dimensions that contribute to the huge diversity of metabolomes and we will illustrate how this diversity shapes the plant in terms of development and performance: (i) temporal regulation: the metabolome is extremely dynamic and temporal changes in the environment can have an immense impact on its composition; (ii) spatial regulation: metabolites can be very specific, in both quantitative and qualitative terms, to specialized organs, tissues, and cell types; (iii) environmental regulation: the metabolic profile of plants is highly dependent on environmental signals, such as light, temperature, and nutrients, and very susceptible to biotic and abiotic stresses; and (iv) genetic regulation: the biosynthesis, structure, and accumulation of metabolites have a genetic origin, and there is quantitative and qualitative variation for metabolomes within a species. We will address the contribution of these dimensions to the wide diversity of metabolomes and highlight how the multi-dimensional regulation of metabolism defines the plant's phenotype.

Environmental regulation of stomatal response in the Arabidopsis Cvi-0 ecotype

The Arabidopsis Cape Verde Islands (Cvi-0) ecotype is known to differ from other ecotypes with respect to environmental stress responses. We analyzed the stomatal behavior of Cvi-0 plants, in response to environmental signals. We investigated the responses of stomatal conductance and aperture to high [CO₂] in the Cvi-0 and Col-0 ecotypes. Cvi-0 showed constitutively higher stomatal conductance and more stomatal opening than Col-0. Cvi-0 stomata opened in response to light, but the response was slow. Under low humidity, stomatal opening was increased in Cvi-0 compared to Col-0. We then assessed whether low humidity affects endogenous ABA levels in Cvi-0. In response to low humidity, Cvi-0 had much higher ABA levels than Col-0. However, epidermal peels experiments showed that Cvi-0 stomata were insensitive to ABA. Measurements of organic and inorganic ions in Cvi-0 guard cell protoplasts indicated an over-accumulation of osmoregulatory anions (malate and Cl⁻). This irregular anion homeostasis in the guard cells may explain the constitutive stomatal opening phenotypes of the Cvi-0 ecotype, which lacks high [CO₂]-induced and low humidity-induced stomatal closure.

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.

Carbon dioxide enrichment inhibits nitrate assimilation in wheat and Arabidopsis

The concentration of carbon dioxide in Earth's atmosphere may double by the end of the 21st century. The response of higher plants to a carbon dioxide doubling often includes a decline in their nitrogen status, but the reasons for this decline have been uncertain. We used five independent methods with wheat and Arabidopsis to show that atmospheric carbon dioxide enrichment inhibited the assimilation of nitrate into organic nitrogen compounds. This inhibition may be largely responsible for carbon dioxide acclimation, the decrease in photosynthesis and growth of plants conducting C(3) carbon fixation after long exposures (days to years) to carbon dioxide enrichment. These results suggest that the relative availability of soil ammonium and nitrate to most plants will become increasingly important in determining their productivity as well as their quality as food.

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).

A focus on natural variation for abiotic constraints response in the model species Arabidopsis thaliana

Plants are particularly subject to environmental stress, as they cannot move from unfavourable surroundings. As a consequence they have to react in situ. In any case, plants have to sense the stress, then the signal has to be transduced to engage the appropriate response. Stress response is effected by regulating genes, by turning on molecular mechanisms to protect the whole organism and its components and/or to repair damage. Reactions vary depending on the type of stress and its intensity, but some are commonly turned on because some responses to different abiotic stresses are shared. In addition, there are multiple ways for plants to respond to environmental stress, depending on the species and life strategy, but also multiple ways within a species depending on plant variety or ecotype. It is regularly accepted that populations of a single species originating from diverse geographic origins and/or that have been subjected to different selective pressure, have evolved retaining the best alleles for completing their life cycle. Therefore, the study of natural variation in response to abiotic stress, can help unravel key genes and alleles for plants to cope with their unfavourable physical and chemical surroundings. This review is focusing on Arabidopsis thaliana which has been largely adopted by the global scientific community as a model organism. Also, tools and data that facilitate investigation of natural variation and abiotic stress encountered in the wild are set out. Characterization of accessions, QTLs detection and cloning of alleles responsible for variation are presented.

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.

Molecular and physiological adaptation to prolonged drought stress in the leaves of two Andean potato genotypes

Responses to prolonged drought and recovery from drought of two South American potato (Solanum tuberosum L. ssp. andigena (Juz & Buk) Hawkes) landraces, Sullu and Ccompis were compared under field conditions. Physiological and biomass measurements, yield analysis, the results of hybridisation to a potato microarray platform (44 000 probes) and metabolite profiling were used to characterise responses to water deficit. Drought affected shoot and root biomass negatively in Ccompis but not in Sullu, whereas both genotypes maintained tuber yield under water stress. Ccompis showed stronger reduction in maximum quantum yield under stress than Sullu, and less decrease in stomatal resistance. Genes associated with PSII functions were activated during recovery in Sullu only. Evidence for sucrose accumulation in Sullu only during maximum stress and recovery was observed, in addition to increases in cell wall biosynthesis. A depression in the abundance of plastid superoxide dismutase transcripts was observed under maximum stress in Ccompis. Both sucrose and the regulatory molecule trehalose accumulated in the leaves of Sullu only. In contrast, in Ccompis, the raffinose oligosaccharide family pathway was activated, whereas low levels of sucrose and minor stress-mediated changes in trehalose were observed. Proline, and expression of the associated genes, rose in both genotypes under drought, with a 3-fold higher increase in Sullu than in Ccompis. The results demonstrate the presence of distinct molecular and biochemical drought responses in the two potato landraces leading to yield maintenance but differential biomass accumulation in vegetative tissues.

Increased protein carbonylation in leaves of Arabidopsis and soybean in response to elevated [CO2]

While exposure of C3 plants to elevated [CO2] would be expected to reduce production of reactive oxygen species (ROS) in leaves because of reduced photorespiratory metabolism, results obtained in the present study suggest that exposure of plants to elevated [CO2] can result in increased oxidative stress. First, in Arabidopsis and soybean, leaf protein carbonylation, a marker of oxidative stress, was often increased when plants were exposed to elevated [CO2]. In soybean, increased carbonyl content was often associated with loss of leaf chlorophyll and reduced enhancement of leaf photosynthetic rate (Pn) by elevated [CO2]. Second, two-dimensional (2-DE) difference gel electrophoresis (DIGE) analysis of proteins extracted from leaves of soybean plants grown at elevated [CO2] or [O3] revealed that both treatments altered the abundance of a similar subset of proteins, consistent with the idea that both conditions may involve an oxidative stress. The 2-DE analysis of leaf proteins was facilitated by a novel and simple procedure to remove ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from soluble soybean leaf extracts. Collectively, these findings add a new dimension to our understanding of global change biology and raise the possibility that oxidative signals can be an unexpected component of plant response to elevated [CO2].

Molecular ecology of global change

Global environmental change is altering the selection regime for all biota. The key selective factors are altered mean, variance and seasonality of climatic variables and increase in CO(2) concentration itself. We review recent studies that document rapid evolution to global climate change at the phenotypic and genetic level, as a response to shifts in these factors. Among the traits that have changed are photoperiod responses, stress tolerance and traits associated with enhanced dispersal. The genetic basis of two traits with a critical role under climate change, stress tolerance and photoperiod behaviour, is beginning to be understood for model organisms, providing a starting point for candidate gene approaches in targeted nonmodel species. Most studies that have documented evolutionary change are correlative, while selection experiments that manipulate relevant variables are rare. The latter are particularly valuable for prediction because they provide insight into heritable change to simulated future conditions. An important gap is that experimental selection regimes have mostly been testing one variable at a time, while synergistic interactions are likely under global change. The expanding toolbox available to molecular ecologists holds great promise for identifying the genetic basis of many more traits relevant to fitness under global change. Such knowledge, in turn, will significantly advance predictions on global change effects because presence and polymorphism of critical genes can be directly assessed. Moreover, knowledge of the genetic architecture of trait correlations will provide the necessary framework for understanding limits to phenotypic evolution; in particular as lack of critical gene polymorphism or entire pathways, metabolic costs of tolerance and linkage or pleiotropy causing negative trait correlations. Synergism among stressor impacts on organismal function may be causally related to conflict among transcriptomic syndromes specific to stressor types. Because adaptation to changing environment is always contingent upon the spatial distribution of genetic variation, high-resolution estimates of gene flow and hybridization should be used to inform predictions of evolutionary rates.

Tuber development phenotypes in adapted and acclimated, drought-stressed Solanum tuberosum ssp. andigena have distinct expression profiles of genes associated with carbon metabolism

A drought screen identified accessions of Solanum tuberosum ssp. andigena that showed varying degrees of physiological acclimation or adaptation to repeated drought stress. The accessions also showed variable tuber phenotypes from small tubers that failed to develop in an accession that showed photosynthetic adaptation to normal tubers in an accession with a phenotype showing some degree of photosynthetic adaptation and acclimation. Using microarray data, we correlated the expression of genes associated with carbon metabolism with the tuber development phenotypes under drought. Genes associated with sucrose and starch metabolism showed responses consistent with starch deficiency in the adapted accession and normal starch deposition in the intermediate accession. Starch phosphorylase and glycogen bound starch synthase were induced in the adapted accession, which had abnormal tuber development. Genes associated with trehalose were induced in the intermediate accession with normal tuber development. Genes associated with respiration were also induced in the intermediate accession, and a pattern compatible with the existence of a 3PGA recovery pathway was revealed. Expression of thioredoxin genes also correlated with tuber development phenotypes under drought stress. The data suggest differential regulation of starch deposition in accessions of Andigena with different abilities to respond to drought stress.

Elevated atmospheric CO(2) concentration and diurnal cycle induce changes in lipid composition in Arabidopsis thaliana

Few studies regarding the effects of elevated atmospheric CO(2) concentrations on plant lipid metabolism have been carried out. Here, the effects of elevated CO(2) concentration on lipid composition in mature seeds and in leaves during the diurnal cycle of Arabidopsis thaliana were investigated. Plants were grown in controlled climate chambers at elevated (800 ppm) and ambient CO(2) concentrations. Lipids were extracted and characterized using thin layer chromatography (TLC) and gas liquid chromatography. The fatty acid profile of total leaf lipids showed large diurnal variations. However, the elevated CO(2) concentration did not induce any significant differences in the diurnal pattern compared with the ambient concentration. The major chloroplast lipids monogalactosyldiacylglycerol (MGDG) and phosphatidylglycerol (PG) were decreased at elevated CO(2) in favour of phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Elevated CO(2) produced a 25% lower ratio of 16:1trans to 16:0 in PG compared with the ambient concentration. With good nutrient supply, growth at elevated CO(2) did not significantly affect single seed weight, total seed mass, oil yield per seed, or the fatty acid profile of the seeds. This study has shown that elevated CO(2) induced changes in leaf lipid composition in A. thaliana, whereas seed lipids were unaffected.