Ethylene-induced differential growth of petioles in Arabidopsis. Analyzing natural variation, response kinetics, and regulation

The role of ethylene in the regulation of plant response mechanisms to waterlogging stress

Waterlogging stands as a common environmental challenge, significantly affecting plant growth, yield, and, in severe cases, survival. In response to waterlogging stress, plants exhibit a series of intricate physiologic, metabolic, and morphologic adaptations. Notably, the gaseous phytohormone ethylene is rapidly accumulated in the plant submerged tissues, assuming an important regulatory factor in plant-waterlogging tolerance. In this review, we summarize recent advances in research on the mechanisms of ethylene in the regulation of plant responses to waterlogging stress. Recent advances found that both ethylene biosynthesis and signal transduction make indispensable contributions to modulating plant adaptation mechanisms to waterlogged condition. Ethylene was also discovered to play an important role in plant physiologic metabolic responses to waterlogging stress, including the energy mechanism, morphologic adaptation, ROS regulation and interactions with other phytohormones. The comprehensive exploration of ethylene and its associated genes provides valuable insights into the precise strategies to leverage ethylene metabolism for enhancing plant resistance to waterlogging stress.

A low-cost open-source imaging platform reveals spatiotemporal insight into leaf elongation and movement

Plant organs move throughout the diurnal cycle, changing leaf and petiole positions to balance light capture, leaf temperature, and water loss under dynamic environmental conditions. Upward movement of the petiole, called hyponasty, is one of several traits of the shade avoidance syndrome (SAS). SAS traits are elicited upon perception of vegetation shade signals such as far-red light (FR) and improve light capture in dense vegetation. Monitoring plant movement at a high temporal resolution allows studying functionality and molecular regulation of hyponasty. However, high temporal resolution imaging solutions are often very expensive, making this unavailable to many researchers. Here, we present a modular and low-cost imaging setup, based on small Raspberry Pi computers that can track leaf movements and elongation growth with high temporal resolution. We also developed an open-source, semiautomated image analysis pipeline. Using this setup, we followed responses to FR enrichment, light intensity, and their interactions. Tracking both elongation and the angle of the petiole, lamina, and entire leaf in Arabidopsis (Arabidopsis thaliana) revealed insight into R:FR sensitivities of leaf growth and movement dynamics and the interactions of R:FR with background light intensity. The detailed imaging options of this system allowed us to identify spatially separate bending points for petiole and lamina positioning of the leaf.

Regulatory mechanism of GA3 application on grape (Vitis vinifera L.) berry size

Gibberellin A3 (GA3) is often used as a principal growth regulator to increase plant size. Here, we applied Tween-20 (2%)-formulated GA3 (T1:40 mg/L; T2:70 mg/L) by dipping the clusters at the initial expansion phase of 'Red Globe' grape (Vitis vinifera L.) in 2018 and 2019. Tween-20 (2%) was used as a control. The results showed that GA3 significantly increased fruit cell length, cell size, diameter, and volume. The hormone levels of auxin (IAA) and zeatin (ZT) were significantly increased at 2 h (0 d) -1 d after application (DAA0-1) and remained significantly higher at DAA1 until maturity. Conversely, ABA exhibited an opposite trend. The mRNA and non-coding sequencing results yielded 436 differentially expressed mRNA (DE_mRNAs), 79 DE_lncRNAs and 17 DE_miRNAs. These genes are linked to hormone pathways like cysteine and methionine metabolism (ko00270), glutathione metabolism (ko00480) and plant hormone signal transduction (ko04075). GA3 application reduced expression of insensitive dwarf 2 (GID2, VIT_07s0129g01000), small auxin-upregulated RNA (SAUR, VIT_08s0007g03120) and 1-aminocyclopropane-1-carboxylate synthase (ACS, VIT_18s0001g08520), but increased SAUR (VIT_04s0023g00560) expression. These four genes were predicted to be negatively regulated by vvi-miR156, vvi-miR172, vvi-miR396, and vvi-miR159, corresponding to specific lncRNAs. Therefore, miRNAs could affect grape size by regulating key genes GID2, ACS and SAUR. The R2R3 MYB family member VvRAX2 (VIT_08s0007g05030) was upregulated in response to GA3 application. Overexpression of VvRAX2 in tomato transgenic lines increased fruit size in contrast to the wild type. This study provides a basis and genetic resources for elucidating the novel role of ncRNAs in fruit development.

Ethylene signaling modulates air humidity responses in plants

Air humidity significantly impacts plant physiology. However, the upstream elements that mediate humidity sensing and adaptive responses in plants remain largely unexplored. In this study, we define high humidity-induced cellular features of Arabidopsis plants and take a quantitative phosphoproteomics approach to obtain a high humidity-responsive landscape of membrane proteins, which we reason are likely the early checkpoints of humidity signaling. We found that a brief high humidity exposure (i.e., 0.5 h) is sufficient to trigger extensive changes in membrane protein abundance and phosphorylation. Enrichment analysis of differentially regulated proteins reveals high humidity-sensitive processes such as 'transmembrane transport', 'response to abscisic acid', and 'stomatal movement'. We further performed a targeted screen of mutants, in which high humidity-responsive pathways/proteins are disabled, to uncover genes mediating high humidity sensitivity. Interestingly, ethylene pathway mutants (i.e., ein2 and ein3eil1) display a range of altered responses, including hyponasty, reactive oxygen species level, and responsive gene expression, to high humidity. Furthermore, we observed a rapid induction of ethylene biosynthesis genes and ethylene evolution after high humidity treatment. Our study sheds light on the potential early signaling events in humidity perception, a fundamental but understudied question in plant biology, and reveals ethylene as a key modulator of high humidity responses in plants.

Light-Dependent High Ambient Temperature-Induced Senescence Assay Using Whole Seedlings

High ambient temperature affects various plant developmental and physiological processes, including senescence. Here, we present a protocol for assaying light-dependent high ambient temperature-induced senescence using whole seedlings. The protocol covers all steps, from inducing senescence by darkness at high ambient temperature to determining the degree of senescence, and includes experimental tips and notes. The onset of senescence is established by quantifying the increased expression of senescence marker genes by quantitative real-time PCR (RT-qPCR). The degree of senescence is determined by measuring the loss of chlorophyll and the increase of ion leakage. This protocol can be adapted to study light-dependent high ambient temperature-induced senescence in other plant species by adjusting the temperature and duration of darkness.

The SlARF4-SlHB8 regulatory module mediates leaf rolling in tomato

Leaf is the main photosynthetic organ in plants and the primary energy source all along the plant life. Given the beneficial role of leaf rolling in improving photosynthetic efficiency and yield in specific environmental conditions, a better understanding of the factors and molecular mechanisms underlying this process is highly suited. Previously, the SlARF4 knocking out mutant exhibited upward curly leaf showed higher resistance to water deficit which driving us to uncover the function of SlARF4 in regulating the curly leaf formation. In this study, we unraveled the unexplored role of the SlARF4-SlHB8 module of transcription factors in the development of leaf rolling. Both SlARF4 loss-of-function and SlHB8 overexpressing tomato plants exhibited upward-rolled leaves, reflecting the active role of the two genes in controlling leaf rolling. Dual-luciferase reporter assays and phenotypic analysis of hybrid progenies suggested that SlHB8 acts downstream of SlARF4 in curly leaf formation. SlARF4 and SlHB8 influence the development of leaf palisade tissues via modulating the expression of genes associated with curly leaf formation. SEM analysis revealed no significant differences in leaf epidermal cells between the two leaf-rolling mutants and the wild type, indicating that curly leaves of arf4 and SlHB8-OE do not result from the asymmetric leaf epidermal cell growth. Our data provide novel insight into the molecular mechanism of abaxial-adaxial determination involving SlARF4 and SlHB8 and reveals that leaf rolling operates via different regulation mechanisms in tomato and Arabidopsis model plant.

Shade-Induced Leaf Senescence in Plants

Leaf senescence is a vital developmental process that involves the orderly breakdown of macromolecules to transfer nutrients from mature leaves to emerging and reproductive organs. This process is essential for a plant's overall fitness. Multiple internal and external factors, such as leaf age, plant hormones, stresses, and light environment, regulate the onset and progression of leaf senescence. When plants grow close to each other or are shaded, it results in significant alterations in light quantity and quality, such as a decrease in photosynthetically active radiation (PAR), a drop in red/far-red light ratios, and a reduction in blue light fluence rate, which triggers premature leaf senescence. Recently, studies have identified various components involved in light, phytohormone, and other signaling pathways that regulate the leaf senescence process in response to shade. This review summarizes the current knowledge on the molecular mechanisms that control leaf senescence induced by shade.

Dissecting the Molecular Regulation of Natural Variation in Growth and Senescence of Two Eutrema salsugineum Ecotypes

Salt cress (Eutrema salsugineum, aka Thellungiella salsuginea) is an extremophile and a close relative of Arabidopsis thaliana. To understand the mechanism of selection of complex traits under natural variation, we analyzed the physiological and proteomic differences between Shandong (SD) and Xinjiang (XJ) ecotypes. The SD ecotype has dark green leaves, short and flat leaves, and more conspicuous taproots, and the XJ ecotype had greater biomass and showed clear signs of senescence or leaf shedding with age. After 2-DE separation and ESI-MS/MS identification, between 25 and 28 differentially expressed protein spots were identified in shoots and roots, respectively. The proteins identified in shoots are mainly involved in cellular metabolic processes, stress responses, responses to abiotic stimuli, and aging responses, while those identified in roots are mainly involved in small-molecule metabolic processes, oxidation-reduction processes, and responses to abiotic stimuli. Our data revealed the evolutionary differences at the protein level between these two ecotypes. Namely, in the evolution of salt tolerance, the SD ecotype highly expressed some stress-related proteins to structurally adapt to the high salt environment in the Yellow River Delta, whereas the XJ ecotype utilizes the specialized energy metabolism to support this evolution of the short-lived xerophytes in the Xinjiang region.

Exogenous ethylene reduces growth via alterations in central metabolism and cell wall composition in tomato (Solanum lycopersicum)

Ethylene is a gaseous hormone with a well-established role in the regulation of plant growth and development. However, its role in the modulation of carbon assimilation and central metabolism remains unclear. Here, we investigated the morphophysiological and biochemical responses of tomato plants (Solanum lycopersicum) following the application of ethylene in the form of ethephon (CEPA - 2-chloroethylphosphonic acid), forcing the classical triple response phenotype. CEPA-treated plants were characterized by growth inhibition, as revealed by significant reductions in both shoot and root dry weights, coupled with a reduced number of leaves and lower specific leaf area. Growth inhibition was associated with a reduction in carbon assimilation due to both lower photosynthesis rates and stomatal conductance, coupled with impairments in carbohydrate turnover. Furthermore, exogenous ethylene led to the accumulation of cell wall compounds (i.e., cellulose and lignin) and phenolics, indicating that exposure to exogenous ethylene also led to changes in specialized metabolism. Collectively, our findings demonstrate that exogenous ethylene disrupts plant growth and leaf structure by affecting both central and specialized metabolism, especially that involved in carbohydrate turnover and cell wall biosynthesis, ultimately leading to metabolic responses that mimic stress situations.

Leaf direction: Lamina joint development and environmental responses

Plant architecture plays a major role in canopy photosynthesis and biomass production, and plants adjust their growth (and thus architecture) in response to changing environments. Leaf angle is one of the most important traits in rice (Oryza sativa L.) plant architecture, because leaf angle strongly affects leaf direction and rice production, with more-erect leaves being advantageous for high-density plantings. The degree of leaf bending depends on the morphology of the lamina joint, which connects the leaf and the sheath. In this review, we discuss cell morphology in different lamina joint tissues and describe the underlying genetic network that governs this morphology and thus regulates leaf direction. Furthermore, we focus on the mechanism by how environmental factors influence rice leaf angle. Our review provides a theoretical framework for the future genetic improvement of rice leaf orientation and plant architecture.

Ethylene-regulated asymmetric growth of the petal base promotes flower opening in rose (Rosa hybrida)

Flowers are the core reproductive structures and key distinguishing features of angiosperms. Flower opening to expose stamens and gynoecia is important in cases where pollinators much be attracted to promote cross-pollination, which can enhance reproductive success and species preservation. The floral opening process is accompanied by the coordinated movement of various floral organs, particularly petals. However, the mechanisms underlying petal movement and flower opening are not well understood. Here, we integrated anatomical, physiological, and molecular approaches to determine the petal movement regulatory network using rose (Rosa hybrida) as a model. We found that PETAL MOVEMENT-RELATED PROTEIN1 (RhPMP1), a homeodomain transcription factor (TF) gene, is a direct target of ETHYLENE INSENSITIVE3, a TF that functions downstream of ethylene signaling. RhPMP1 expression was upregulated by ethylene and specifically activated endoreduplication of parenchyma cells on the adaxial side of the petal (ADSP) base by inducing the expression of RhAPC3b, a gene encoding the core subunit of the Anaphase-Promoting Complex. Cell expansion of the parenchyma on the ADSP base was subsequently enhanced, thus resulting in asymmetric growth of the petal base, leading to the typical epinastic movement of petals and flower opening. These findings provide insights into the pathway regulating petal movement and associated flower-opening mechanisms.�.

The Oxidative Paradox in Low Oxygen Stress in Plants

Reactive oxygen species (ROS) are part of aerobic environments, and variations in the availability of oxygen (O2) in the environment can lead to altered ROS levels. In plants, the O2 sensing machinery guides the molecular response to low O2, regulating a subset of genes involved in metabolic adaptations to hypoxia, including proteins involved in ROS homeostasis and acclimation. In addition, nitric oxide (NO) participates in signaling events that modulate the low O2 stress response. In this review, we summarize recent findings that highlight the roles of ROS and NO under environmentally or developmentally defined low O2 conditions. We conclude that ROS and NO are emerging regulators during low O2 signalling and key molecules in plant adaptation to flooding conditions.

Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature

Organs such as hypocotyls and petioles rapidly elongate in response to shade and temperature cues, contributing to adaptive responses that improve plant fitness. Growth plasticity in these organs is achieved through a complex network of molecular signals. Besides conveying information from the environment, this signaling network also transduces internal signals, such as those associated with the circadian clock. A number of studies performed in Arabidopsis hypocotyls, and to a lesser degree in petioles, have been informative for understanding the signaling networks that regulate elongation of aerial plant organs. In particular, substantial progress has been made towards understanding the molecular mechanisms that regulate responses to light, the circadian clock, and temperature. Signals derived from these three stimuli converge on the BAP module, a set of three different types of transcription factors that interdependently promote gene transcription and growth. Additional key positive regulators of growth that are also affected by environmental cues include the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) E3 ubiquitin ligase proteins. In this review we summarize the key signaling pathways that regulate the growth of hypocotyls and petioles, focusing specifically on molecular mechanisms important for transducing signals derived from light, the circadian clock, and temperature. While it is clear that similarities abound between the signaling networks at play in these two organs, there are also important differences between the mechanisms regulating growth in hypocotyls and petioles.

Uncharted routes: exploring the relevance of auxin movement via plasmodesmata

Auxin is an endogenous small molecule with an incredibly large impact on growth and development in plants. Movement of auxin between cells, due to its negative charge at most physiological pHs, strongly relies on families of active transporters. These proteins import auxin from the extracellular space or export it into the same. Mutations in these components have profound impacts on biological processes. Another transport route available to auxin, once the substance is inside the cell, are plasmodesmata connections. These small channels connect the cytoplasms of neighbouring plant cells and enable flow between them. Interestingly, the biological significance of this latter mode of transport is only recently starting to emerge with examples from roots, hypocotyls and leaves. The existence of two transport systems provides opportunities for reciprocal cross-regulation. Indeed, auxin levels influence proteins controlling plasmodesmata permeability, while cell-cell communication affects auxin biosynthesis and transport. In an evolutionary context, transporter driven cell-cell auxin movement and plasmodesmata seem to have evolved around the same time in the green lineage. This highlights a co-existence from early on and a likely functional specificity of the systems. Exploring more situations where auxin movement via plasmodesmata has relevance for plant growth and development, and clarifying the regulation of such transport, will be key aspects in coming years.This article has an associated Future Leader to Watch interview with the author of the paper.

All roads lead to growth: imaging-based and biochemical methods to measure plant growth

Plant growth is a highly complex biological process that involves innumerable interconnected biochemical and signalling pathways. Many different techniques have been developed to measure growth, unravel the various processes that contribute to plant growth, and understand how a complex interaction between genotype and environment determines the growth phenotype. Despite this complexity, the term 'growth' is often simplified by researchers; depending on the method used for quantification, growth is viewed as an increase in plant or organ size, a change in cell architecture, or an increase in structural biomass. In this review, we summarise the cellular and molecular mechanisms underlying plant growth, highlight state-of-the-art imaging and non-imaging-based techniques to quantitatively measure growth, including a discussion of their advantages and drawbacks, and suggest a terminology for growth rates depending on the type of technique used.

Circadian leaf movements facilitate overtopping of neighbors

Many plants exhibit circadian clock-driven leaf movements whereby the leaves are raised during the day to achieve a relatively high angle during the evening, before lowering late in the night. Such leaf movements were first recorded over 2000 years ago but there is still much debate as to their purpose. We investigated whether such leaf movements within Arabidopsis, a ruderal rosette plant, can aid in overtopping leaves of neighboring plants. Wild type and circadian clock mutant plants were grown in an alternating grid system so that their leaves would meet as the plants grew. Experiments were performed using day lengths that matched the endogenous rhythm of either wild type or mutant. Plants grown in a day length shorter than their endogenous rhythm were consistently overtopped by plants which were in synchrony with the day night cycle, demonstrating a clear overtopping advantage resulting from circadian leaf movement rhythms. Furthermore, we found that this leaf overtopping as a result of correctly synchronized circadian leaf movements is additive to leaf overtopping due to shade avoidance. Curiously, this did not apply to plants grown in a day length longer than their endogenous period. Plants grown in a day length longer than their endogenous period were able to adapt their leaf rhythms and suffered no overtopping disadvantage. Crucially, our results show that, in a context-dependent manner, circadian clock-driven leaf movements in resonance with the external light/dark cycle can facilitate overtopping of the leaves of neighboring plants.

Shade delays flowering in Medicago sativa

Shade-intolerant plants respond to the decrease in the red (R) to far-red (FR) light ratio (R:FR) occurring under shade by elongating stems and petioles and by re-positioning leaves, in a race to outcompete neighbors for the sunlight resource. In some annual species, the shade avoidance syndrome (SAS) is accompanied by the early induction of flowering. Anticipated flowering is viewed as a strategy to set seeds before the resources become severely limiting. Little is known about the molecular mechanisms of SAS in perennial forage crops like alfalfa (Medicago sativa). To study SAS in alfalfa, we exposed alfalfa plants to simulated shade by supplementing with FR light. Low R:FR light produced a classical SAS, with increased internode and petiole lengths, but unexpectedly also with delayed flowering. To understand the molecular mechanisms involved in uncoupling SAS from early flowering, we used a transcriptomic approach. The SAS is likely to be mediated by increased expression of msPIF3 and msHB2 in low R:FR light. Constitutive expression of these genes in Arabidopsis led to SAS, including early flowering, strongly suggesting that their roles are conserved. Delayed flowering was likely to be mediated by the downregulation of msSPL3, which promotes flowering in both Arabidopsis and alfalfa. Shade-delayed flowering in alfalfa may be important to extend the vegetative phase under suboptimal light conditions, and thus assure the accumulation of reserves necessary to resume growth after the next season.

Elevated carbon dioxide plus chronic warming causes dramatic increases in leaf angle in tomato, which correlates with reduced plant growth

Limited evidence indicates that moderate leaf hyponasty can be induced by high temperatures or unnaturally high CO₂ . Here, we report that the combination of warming plus elevated CO₂ (eCO₂ ) induces severe leaf hyponasty in tomato (Solanum lycopersicum L.). To characterize this phenomenon, tomato plants were grown at two levels of CO₂ (400 vs. 700 ppm) and two temperature regimes (30 vs. 37°C) for 16-18 days. Leaf hyponasty increased dramatically with warming plus eCO₂ but increased only slightly with either factor alone and was slowly reversible upon transfer to control treatments. Increases in leaf angle were not correlated with leaf temperature, leaf water stress, or heat-related damage to photosynthesis. However, steeper leaf angles were correlated with decreases in leaf area and biomass, which could be explained by decreased light interception and thus in situ photosynthesis, as leaves became more vertical. Petiole hyponasty and leaf-blade cupping were also observed with warming + eCO₂ in marigold and soybean, respectively, which are compound-leaved species like tomato, but no such hyponasty was observed in sunflower and okra, which have simple leaves. If severe leaf hyponasty is common under eCO₂ and warming, then this may have serious consequences for food production in the future.

Hypoxia and the group VII ethylene response transcription factor HRE2 promote adventitious root elongation in Arabidopsis

Soil water-logging and flooding are common environmental stress conditions that can impair plant fitness. Roots are the first organs to be confronted with reduced oxygen tension as a result of flooding. While anatomical and morphological adaptations of roots are extensively studied, the root system architecture is only now becoming a focus of flooding research. Adventitious root (AR) formation shifts the root system higher up the plant, thereby facilitating supply with oxygen, and thus improving root and plant survival. We used Arabidopsis knockout mutants and overexpressors of ERFVII transcription factors to study their role in AR formation under hypoxic conditions and in response to ethylene. Results show that ethylene inhibits AR formation. Hypoxia mainly promotes AR elongation rather than formation mediated by ERFVII transcription factors, as indicated by reduced AR elongation in erfVII seedlings. Overexpression of HRE2 induces AR elongation to the same degree as hypoxia, while ethylene overrides HRE2-induced AR elongation. The ERFVII transcription factors promote establishment of an AR system that is under negative control by ethylene. Inhibition of growth of the main root system and promotion of AR elongation under hypoxia strengthens the root system in upper soil layers where oxygen shortage may last for shorter time periods.

Far-Red Light Detection in the Shoot Regulates Lateral Root Development through the HY5 Transcription Factor

Plants in dense vegetation compete for resources and detect competitors through reflection of far-red (FR) light from surrounding plants. This reflection causes a reduced red (R):FR ratio, which is sensed through phytochromes. Low R:FR induces shade avoidance responses of the shoot and also changes the root system architecture, although this has received little attention so far. Here, we investigate the molecular mechanisms through which light detection in the shoot regulates root development in Arabidopsis thaliana We do so using a combination of microscopy, gene expression, and mutant study approaches in a setup that allows root imaging without exposing the roots to light treatment. We show that low R:FR perception in the shoot decreases the lateral root (LR) density by inhibiting LR emergence. This decrease in LR emergence upon shoot FR enrichment is regulated by phytochrome-dependent accumulation of the transcription factor ELONGATED HYPOCOTYL5 (HY5) in the LR primordia. HY5 regulates LR emergence by decreasing the plasma membrane abundance of PIN-FORMED3 and LIKE-AUX1 3 auxin transporters. Accordingly, FR enrichment reduces the auxin signal in the overlaying cortex cells, and this reduces LR outgrowth. This shoot-to-root communication can help plants coordinate resource partitioning under competition for light in high density fields.

Comprehensive analysis of response and tolerant mechanisms in early-stage soybean at initial-flooding stress

Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, which markedly reduces its growth and yield. Morphological and biochemical changes such as an increase of fresh weight and a decrease of ATP content happen in early-stage soybean at initial-flooding stress, indicating that soybean responses to flooding stress are keys for its survival and seedling growth. Phosphoproteomics and nuclear proteomics are useful tools to detect protein-phosphorylation status and to identify transcriptional factors. In the review, the effect of flooding on soybean response to initial flooding stress is discussed based on recent results of proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies. In addition, soybean survival under flooding stress, which is defined as tolerance mechanism, is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean.

BIOLOGICAL SIGNIFICANCE

Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, especially soybean responses to initial flooding stress is key for its survival and seedling growth. Recently, proteomic techniques are applied to investigate the response and tolerant mechanisms of soybean at initial flooding condition. In this review, the progress in proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies about the initial-flooding response mechanism in early-stage soybean is presented. In addition, the tolerant mechanism in soybean is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. Through this review, the key proteins and genes involved in initial flooding response and tolerance at early stage soybean are summarized and they contribute greatly to uncover response and tolerance mechanism at early stage under stressful environmental conditions in soybean.

Ethylene Role in Plant Growth, Development and Senescence: Interaction with Other Phytohormones

The complex juvenile/maturity transition during a plant's life cycle includes growth, reproduction, and senescence of its fundamental organs: leaves, flowers, and fruits. Growth and senescence of leaves, flowers, and fruits involve several genetic networks where the phytohormone ethylene plays a key role, together with other hormones, integrating different signals and allowing the onset of conditions favorable for stage progression, reproductive success and organ longevity. Changes in ethylene level, its perception, and the hormonal crosstalk directly or indirectly regulate the lifespan of plants. The present review focused on ethylene's role in the development and senescence processes in leaves, flowers and fruits, paying special attention to the complex networks of ethylene crosstalk with other hormones. Moreover, aspects with limited information have been highlighted for future research, extending our understanding on the importance of ethylene during growth and senescence and boosting future research with the aim to improve the qualitative and quantitative traits of crops.

Time-Lapse Imaging to Examine the Growth Kinetics of Arabidopsis Seedlings in Response to Ethylene

Ethylene is well known to inhibit the growth of dark-grown eudicot seedlings. Most studies examine this inhibition after several days of exposure to ethylene. However, such end-point analysis misses transient responses and the dynamic nature of growth regulation. Here, high-resolution, time-lapse imaging is described as a method to gather data about ethylene growth kinetics and movement responses of the hypocotyls of dark-grown seedlings of Arabidopsis thaliana. These methods allow for the characterization of short-term kinetic responses and can be modified for the analysis of roots and seedlings from other species.

Molecular and genetic control of plant thermomorphogenesis

Temperature is a major factor governing the distribution and seasonal behaviour of plants. Being sessile, plants are highly responsive to small differences in temperature and adjust their growth and development accordingly. The suite of morphological and architectural changes induced by high ambient temperatures, below the heat-stress range, is collectively called thermomorphogenesis. Understanding the molecular genetic circuitries underlying thermomorphogenesis is particularly relevant in the context of climate change, as this knowledge will be key to rational breeding for thermo-tolerant crop varieties. Until recently, the fundamental mechanisms of temperature perception and signalling remained unknown. Our understanding of temperature signalling is now progressing, mainly by exploiting the model plant Arabidopsis thaliana. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) has emerged as a critical player in regulating phytohormone levels and their activity. To control thermomorphogenesis, multiple regulatory circuits are in place to modulate PIF4 levels, activity and downstream mechanisms. Thermomorphogenesis is integrally governed by various light signalling pathways, the circadian clock, epigenetic mechanisms and chromatin-level regulation. In this Review, we summarize recent progress in the field and discuss how the emerging knowledge in Arabidopsis may be transferred to relevant crop systems.

Ethylene and Hormonal Cross Talk in Vegetative Growth and Development

Ethylene is a gaseous plant hormone that most likely became a functional hormone during the evolution of charophyte green algae, prior to land colonization. From this ancient origin, ethylene evolved into an important growth regulator that is essential for myriad plant developmental processes. In vegetative growth, ethylene appears to have a dual role, stimulating and inhibiting growth, depending on the species, tissue, and cell type, developmental stage, hormonal status, and environmental conditions. Moreover, ethylene signaling and response are part of an intricate network in cross talk with internal and external cues. Besides being a crucial factor in the growth control of roots and shoots, ethylene can promote flowering, fruit ripening and abscission, as well as leaf and petal senescence and abscission and, hence, plays a role in virtually every phase of plant life. Last but not least, together with jasmonates, salicylate, and abscisic acid, ethylene is important in steering stress responses.

Ethylene-Mediated Acclimations to Flooding Stress

Flooding is detrimental for plants, primarily because of restricted gas exchange underwater, which leads to an energy and carbohydrate deficit. Impeded gas exchange also causes rapid accumulation of the volatile ethylene in all flooded plant cells. Although several internal changes in the plant can signal the flooded status, it is the pervasive and rapid accumulation of ethylene that makes it an early and reliable flooding signal. Not surprisingly, it is a major regulator of several flood-adaptive plant traits. Here, we discuss these major ethylene-mediated traits, their functional relevance, and the recent progress in identifying the molecular and signaling events underlying these traits downstream of ethylene. We also speculate on the role of ethylene in postsubmergence recovery and identify several questions for future investigations.

Ethylene-Mediated Regulation of A2-Type CYCLINs Modulates Hyponastic Growth in Arabidopsis

Upward leaf movement (hyponastic growth) is frequently observed in response to changing environmental conditions and can be induced by the phytohormone ethylene. Hyponasty results from differential growth (i.e. enhanced cell elongation at the proximal abaxial side of the petiole relative to the adaxial side). Here, we characterize Enhanced Hyponasty-d, an activation-tagged Arabidopsis (Arabidopsis thaliana) line with exaggerated hyponasty. This phenotype is associated with overexpression of the mitotic cyclin CYCLINA2;1 (CYCA2;1), which hints at a role for cell divisions in regulating hyponasty. Indeed, mathematical analysis suggested that the observed changes in abaxial cell elongation rates during ethylene treatment should result in a larger hyponastic amplitude than observed, unless a decrease in cell proliferation rate at the proximal abaxial side of the petiole relative to the adaxial side was implemented. Our model predicts that when this differential proliferation mechanism is disrupted by either ectopic overexpression or mutation of CYCA2;1, the hyponastic growth response becomes exaggerated. This is in accordance with experimental observations on CYCA2;1 overexpression lines and cyca2;1 knockouts. We therefore propose a bipartite mechanism controlling leaf movement: ethylene induces longitudinal cell expansion in the abaxial petiole epidermis to induce hyponasty and simultaneously affects its amplitude by controlling cell proliferation through CYCA2;1. Further corroborating the model, we found that ethylene treatment results in transcriptional down-regulation of A2-type CYCLINs and propose that this, and possibly other regulatory mechanisms affecting CYCA2;1, may contribute to this attenuation of hyponastic growth.

Red:far-red light conditions affect the emission of volatile organic compounds from barley (Hordeum vulgare), leading to altered biomass allocation in neighbouring plants

BACKGROUND AND AIMS

Volatile organic compounds (VOCs) play various roles in plant-plant interactions, and constitutively produced VOCs might act as a cue to sense neighbouring plants. Previous studies have shown that VOCs emitted from the barley (Hordeum vulgare) cultivar 'Alva' cause changes in biomass allocation in plants of the cultivar 'Kara'. Other studies have shown that shading and the low red:far-red (R:FR) conditions that prevail at high plant densities can reduce the quantity and alter the composition of the VOCs emitted by Arabidopsis thaliana, but whether this affects plant-plant signalling remains unknown. This study therefore examines the effects of far-red light enrichment on VOC emissions and plant-plant signalling between 'Alva' and 'Kara'.

METHODS

The proximity of neighbouring plants was mimicked by supplemental far-red light treatment of VOC emitter plants of barley grown in growth chambers. Volatiles emitted by 'Alva' under control and far-red light-enriched conditions were analysed using gas chromatography-mass spectrometry (GC-MS). 'Kara' plants were exposed to the VOC blend emitted by the 'Alva' plants that were subjected to either of the light treatments. Dry matter partitioning, leaf area, stem and total root length were determined for 'Kara' plants exposed to 'Alva' VOCs, and also for 'Alva' plants exposed to either control or far-red-enriched light treatments.

KEY RESULTS

Total VOC emissions by 'Alva' were reduced under low R:FR conditions compared with control light conditions, although individual volatile compounds were found to be either suppressed, induced or not affected by R:FR. The altered composition of the VOC blend emitted by 'Alva' plants exposed to low R:FR was found to affect carbon allocation in receiver plants of 'Kara'.

CONCLUSIONS

The results indicate that changes in R:FR light conditions influence the emissions of VOCs in barley, and that these altered emissions affect VOC-mediated plant-plant interactions.

Phytotyping(4D) : a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth

Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D) , we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants.

Shade avoidance components and pathways in adult plants revealed by phenotypic profiling

Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.

AtGGM2014, an Arabidopsis gene co-expression network for functional studies

Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the ArrayExpress database, we constructed an Arabidopsis gene co-expression network, termed AtGGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. AtGGM2014 offers a constructive tool for plant systems biology studies.

Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress

Flooding has severe negative effects on soybean growth. To explore the flooding-responsive mechanisms in early-stage soybean, a phosphoproteomic approach was used. Two-day-old soybean plants were treated without or with flooding for 3, 6, 12, and 24 h, and root tip proteins were then extracted and analyzed at each time point. After 3 h of flooding exposure, the fresh weight of soybeans increased, whereas the ATP content of soybean root tips decreased. Using a gel-free proteomic technique, a total of 114 phosphoproteins were identified in the root tip samples, and 34 of the phosphoproteins were significantly changed with respect to phosphorylation status after 3 h of flooding stress. Among these phosphoproteins, eukaryotic translation initiation factors were dephosphorylated, whereas several protein synthesis-related proteins were phosphorylated. The mRNA expression levels of sucrose phosphate synthase 1F and eukaryotic translation initiation factor 4 G were down-regulated, whereas UDP-glucose 6-dehydrogenase mRNA expression was up-regulated during growth but down-regulated under flooding stress. Furthermore, bioinformatic protein interaction analysis of flooding-responsive proteins based on temporal phosphorylation patterns indicated that eukaryotic translation initiation factor 4 G was located in the center of the network during flooding. Soybean eukaryotic translation initiation factor 4 G has homology to programmed cell death 4 protein and is implicated in ethylene signaling. The weight of soybeans was increased with treatment by an ethylene-releasing agent under flooding condition, but it was decreased when plants were exposed to an ethylene receptor antagonist. These results suggest that the ethylene signaling pathway plays an important role, via the protein phosphorylation, in mechanisms of plant tolerance to the initial stages of flooding stress in soybean root tips.

Shade avoidance: phytochrome signalling and other aboveground neighbour detection cues

Plants compete with neighbouring vegetation for limited resources. In competition for light, plants adjust their architecture to bring the leaves higher in the vegetation where more light is available than in the lower strata. These architectural responses include accelerated elongation of the hypocotyl, internodes and petioles, upward leaf movement (hyponasty), and reduced shoot branching and are collectively referred to as the shade avoidance syndrome. This review discusses various cues that plants use to detect the presence and proximity of neighbouring competitors and respond to with the shade avoidance syndrome. These cues include light quality and quantity signals, mechanical stimulation, and plant-emitted volatile chemicals. We will outline current knowledge about each of these signals individually and discuss their possible interactions. In conclusion, we will make a case for a whole-plant, ecophysiology approach to identify the relative importance of the various neighbour detection cues and their possible interactions in determining plant performance during competition.

Interactions between auxin, microtubules and XTHs mediate green shade- induced petiole elongation in arabidopsis

Plants are highly attuned to translating environmental changes to appropriate modifications in growth. Such phenotypic plasticity is observed in dense vegetations, where shading by neighboring plants, triggers rapid unidirectional shoot growth (shade avoidance), such as petiole elongation, which is partly under the control of auxin. This growth is fuelled by cellular expansion requiring cell-wall modification by proteins such as xyloglucan endotransglucosylase/hydrolases (XTHs). Cortical microtubules (cMTs) are highly dynamic cytoskeletal structures that are also implicated in growth regulation. The objective of this study was to investigate the tripartite interaction between auxin, cMTs and XTHs in shade avoidance. Our results indicate a role for cMTs to control rapid petiole elongation in Arabidopsis during shade avoidance. Genetic and pharmacological perturbation of cMTs obliterated shade-induced growth and led to a reduction in XTH activity as well. Furthermore, the cMT disruption repressed the shade-induced expression of a specific set of XTHs. These XTHs were also regulated by the hormone auxin, an important regulator of plant developmental plasticity and also of several shade avoidance responses. Accordingly, the effect of cMT disruption on the shade enhanced XTH expression could be rescued by auxin application. Based on the results we hypothesize that cMTs can mediate petiole elongation during shade avoidance by regulating the expression of cell wall modifying proteins via control of auxin distribution.

NAC transcription factor speedy hyponastic growth regulates flooding-induced leaf movement in Arabidopsis

In rosette plants, root flooding (waterlogging) triggers rapid upward (hyponastic) leaf movement representing an important architectural stress response that critically determines plant performance in natural habitats. The directional growth is based on localized longitudinal cell expansion at the lower (abaxial) side of the leaf petiole and involves the volatile phytohormone ethylene (ET). We report the existence of a transcriptional core unit underlying directional petiole growth in Arabidopsis thaliana, governed by the NAC transcription factor speedy hyponastic growth (SHYG). Overexpression of SHYG in transgenic Arabidopsis thaliana enhances waterlogging-triggered hyponastic leaf movement and cell expansion in abaxial cells of the basal petiole region, while both responses are largely diminished in shyg knockout mutants. Expression of several expansin and xyloglucan endotransglycosylase/hydrolase genes encoding cell wall-loosening proteins was enhanced in SHYG overexpressors but lowered in shyg. We identified ACC oxidase5 (ACO5), encoding a key enzyme of ET biosynthesis, as a direct transcriptional output gene of SHYG and found a significantly reduced leaf movement in response to root flooding in aco5 T-DNA insertion mutants. Expression of SHYG in shoot tissue is triggered by root flooding and treatment with ET, constituting an intrinsic ET-SHYG-ACO5 activator loop for rapid petiole cell expansion upon waterlogging.

Diverse roles of ERECTA family genes in plant development

Multiple receptor-like kinases (RLKs) enable intercellular communication that coordinates growth and development of plant tissues. ERECTA family receptors (ERfs) are an ancient family of leucine-rich repeat RLKs that in Arabidopsis consists of three genes: ERECTA, ERL1, and ERL2. ERfs sense secreted cysteine-rich peptides from the EPF/EPFL family and transmit the signal through a MAP kinase cascade. This review discusses the functions of ERfs in stomata development, in regulation of longitudinal growth of aboveground organs, during reproductive development, and in the shoot apical meristem. In addition the role of ERECTA in plant responses to biotic and abiotic factors is examined. Elena D. Shpak (Corresponding author).

Canopy light cues affect emission of constitutive and methyl jasmonate-induced volatile organic compounds in Arabidopsis thaliana

The effects of plant competition for light on the emission of plant volatile organic compounds (VOCs) were studied by investigating how different light qualities that occur in dense vegetation affect the emission of constitutive and methyl-jasmonate-induced VOCs. Arabidopsis thaliana Columbia (Col-0) plants and Pieris brassicae caterpillars were used as a biological system to study the effects of light quality manipulations on VOC emissions and attraction of herbivores. VOCs were analysed using gas chromatography-mass spectrometry and the effects of light quality, notably the red : far red light ratio (R : FR), on expression of genes associated with VOC production were studied using reverse transcriptase-quantitative PCR. The emissions of both constitutive and methyl-jasmonate-induced green leaf volatiles and terpenoids were partially suppressed under low R : FR and severe shading conditions. Accordingly, the VOC-based preference of neonates of the specialist lepidopteran herbivore P. brassicae was significantly affected by the R : FR ratio. We conclude that VOC-mediated interactions among plants and between plants and organisms at higher trophic levels probably depend on light alterations caused by nearby vegetation. Studies on plant-plant and plant-insect interactions through VOCs should take into account the light quality within dense stands when extrapolating to natural and agricultural field conditions.

Flooding of the apoplast is a key factor in the development of hyperhydricity

The physiological disorder hyperhydricity occurs frequently in tissue culture and causes several morphological abnormalities such as thick, brittle, curled, and translucent leaves. It is well known that hyperhydric shoots are characterized by a high water content, but how this is related to the abnormalities is not clear. It was observed that water accumulated extensively in the apoplast of leaves of hyperhydric Arabidopsis seedlings and flooded apoplastic air spaces almost completely. In hyperhydric Arabidopsis seedlings, the volume of apoplastic air was reduced from 85% of the apoplast to only 15%. Similar results were obtained with hyperhydric shoots of statice. The elevated expression of hypoxia-responsive genes in hyperhydric seedlings showed that the water saturation of the apoplast decreased oxygen supply. This demonstrates a reduced gas exchange between the symplast and its surroundings, which will consequently lead to the accumulation of gases in the symplast, for example ethylene and methyl jasmonate. The impairment of gas exchange probably brings about the symptoms of hyperhydricity. Interestingly, stomatal aperture was reduced in hyperhydric plants, a previously reported response to injection of water into the apoplast. Closure of the stomata and the accumulation of water in the apoplast may be the reasons why seedlings with a low level of hyperhydricity showed improved acclimatization after planting into soil.

Antiphase light and temperature cycles affect PHYTOCHROME B-controlled ethylene sensitivity and biosynthesis, limiting leaf movement and growth of Arabidopsis

In the natural environment, days are generally warmer than the night, resulting in a positive day/night temperature difference (+DIF). Plants have adapted to these conditions, and when exposed to antiphase light and temperature cycles (cold photoperiod/warm night [-DIF]), most species exhibit reduced elongation growth. To study the physiological mechanism of how light and temperature cycles affect plant growth, we used infrared imaging to dissect growth dynamics under +DIF and -DIF in the model plant Arabidopsis (Arabidopsis thaliana). We found that -DIF altered leaf growth patterns, decreasing the amplitude and delaying the phase of leaf movement. Ethylene application restored leaf growth in -DIF conditions, and constitutive ethylene signaling mutants maintain robust leaf movement amplitudes under -DIF, indicating that ethylene signaling becomes limiting under these conditions. In response to -DIF, the phase of ethylene emission advanced 2 h, but total ethylene emission was not reduced. However, expression analysis on members of the 1-aminocyclopropane-1-carboxylic acid (ACC) synthase ethylene biosynthesis gene family showed that ACS2 activity is specifically suppressed in the petiole region under -DIF conditions. Indeed, petioles of plants under -DIF had reduced ACC content, and application of ACC to the petiole restored leaf growth patterns. Moreover, acs2 mutants displayed reduced leaf movement under +DIF, similar to wild-type plants under -DIF. In addition, we demonstrate that the photoreceptor PHYTOCHROME B restricts ethylene biosynthesis and constrains the -DIF-induced phase shift in rhythmic growth. Our findings provide a mechanistic insight into how fluctuating temperature cycles regulate plant growth.

Transcriptomic and physiological variations of three Arabidopsis ecotypes in response to salt stress

Salt stress is one of the major abiotic stresses in agriculture worldwide. Analysis of natural genetic variation in Arabidopsis is an effective approach to characterize candidate salt responsive genes. Differences in salt tolerance of three Arabidopsis ecotypes were compared in this study based on their responses to salt treatments at two developmental stages: seed germination and later growth. The Sha ecotype had higher germination rates, longer roots and less accumulation of superoxide radical and hydrogen peroxide than the Ler and Col ecotypes after short term salt treatment. With long term salt treatment, Sha exhibited higher survival rates and lower electrolyte leakage. Transcriptome analysis revealed that many genes involved in cell wall, photosynthesis, and redox were mainly down-regulated by salinity effects, while transposable element genes, microRNA and biotic stress related genes were significantly changed in comparisons of Sha vs. Ler and Sha vs. Col. Several pathways involved in tricarboxylic acid cycle, hormone metabolism and development, and the Gene Ontology terms involved in response to stress and defense response were enriched after salt treatment, and between Sha and other two ecotypes. Collectively, these results suggest that the Sha ecotype is preconditioned to withstand abiotic stress. Further studies about detailed gene function are needed. These comparative transcriptomic and analytical results also provide insight into the complexity of salt stress tolerance mechanisms.

Perception of low red:far-red ratio compromises both salicylic acid- and jasmonic acid-dependent pathogen defences in Arabidopsis

In dense stands of plants, such as agricultural monocultures, plants are exposed simultaneously to competition for light and other stresses such as pathogen infection. Here, we show that both salicylic acid (SA)-dependent and jasmonic acid (JA)-dependent disease resistance is inhibited by a simultaneously reduced red:far-red light ratio (R:FR), the early warning signal for plant competition. Conversely, SA- and JA-dependent induced defences did not affect shade-avoidance responses to low R:FR. Reduced pathogen resistance by low R:FR was accompanied by a strong reduction in the regulation of JA- and SA-responsive genes. The severe inhibition of SA-responsive transcription in low R:FR appeared to be brought about by the repression of SA-inducible kinases. Phosphorylation of the SA-responsive transcription co-activator NPR1, which is required for full induction of SA-responsive transcription, was indeed reduced and may thus play a role in the suppression of SA-mediated defences by low R:FR-mediated phytochrome inactivation. Our results indicate that foraging for light through the shade-avoidance response is prioritised over plant immune responses when plants are simultaneously challenged with competition and pathogen attack.

Phenotyping the kinematics of leaf development in flowering plants: recommendations and pitfalls

Leaves of flowering plants are produced from the shoot apical meristem at regular intervals and they grow according to a developmental program that is determined by both genetic and environmental factors. Detailed frameworks for multiscale dynamic analyses of leaf growth have been developed in order to identify and interpret phenotypic differences caused by either genetic or environmental variations. They revealed that leaf growth dynamics are non-linearly and nonhomogeneously distributed over the lamina, in the leaf tissues and cells. The analysis of the variability in leaf growth, and its underlying processes, has recently gained momentum with the development of automated phenotyping platforms that use various technologies to record growth at different scales and at high throughput. These modern tools are likely to accelerate the characterization of gene function and the processes that underlie the control of shoot development. Combined with powerful statistical analyses, trends have emerged that may have been overlooked in low throughput analyses. However, in many examples, the increase in throughput allowed by automated platforms has led to a decrease in the spatial and/or temporal resolution of growth analyses. Concrete examples presented here indicate that simplification of the dynamic leaf system, without consideration of its spatial and temporal context, can lead to important misinterpretations of the growth phenotype.

Natural variation identifies multiple loci controlling petal shape and size in Arabidopsis thaliana

Natural variation in organ morphologies can have adaptive significance and contribute to speciation. However, the underlying allelic differences responsible for variation in organ size and shape remain poorly understood. We have utilized natural phenotypic variation in three Arabidopsis thaliana ecotypes to examine the genetic basis for quantitative variation in petal length, width, area, and shape. We identified 23 loci responsible for such variation, many of which appear to correspond to genes not previously implicated in controlling organ morphology. These analyses also demonstrated that allelic differences at distinct loci can independently affect petal length, width, area or shape, suggesting that these traits behave as independent modules. We also showed that ERECTA (ER), encoding a leucine-rich repeat (LRR) receptor-like serine-threonine kinase, is a major effect locus determining petal shape. Allelic variation at the ER locus was associated with differences in petal cell proliferation and concomitant effects on petal shape. ER has been previously shown to be required for regulating cell division and expansion in other contexts; the ER receptor-like kinase functioning to also control organ-specific proliferation patterns suggests that allelic variation in common signaling components may nonetheless have been a key factor in morphological diversification.

Genetical Genomics Reveals Large Scale Genotype-By-Environment Interactions in Arabidopsis thaliana

One of the major goals of quantitative genetics is to unravel the complex interactions between molecular genetic factors and the environment. The effects of these genotype-by-environment interactions also affect and cause variation in gene expression. The regulatory loci responsible for this variation can be found by genetical genomics that involves the mapping of quantitative trait loci (QTLs) for gene expression traits also called expression-QTL (eQTLs). Most genetical genomics experiments published so far, are performed in a single environment and hence do not allow investigation of the role of genotype-by-environment interactions. Furthermore, most studies have been done in a steady state environment leading to acclimated expression patterns. However a response to the environment or change therein can be highly plastic and possibly lead to more and larger differences between genotypes. Here we present a genetical genomics study on 120 Arabidopsis thaliana, Landsberg erecta × Cape Verde Islands, recombinant inbred lines (RILs) in active response to the environment by treating them with 3 h of shade. The results of this experiment are compared to a previous study on seedlings of the same RILs from a steady state environment. The combination of two highly different conditions but exactly the same RILs with a fixed genetic variation showed the large role of genotype-by-environment interactions on gene expression levels. We found environment-dependent hotspots of transcript regulation. The major hotspot was confirmed by the expression profile of a near isogenic line. Our combined analysis leads us to propose CSN5A, a COP9 signalosome component, as a candidate regulator for the gene expression response to shade.

Ethylene promotes hyponastic growth through interaction with ROTUNDIFOLIA3/CYP90C1 in Arabidopsis

Upward leaf movement, called hyponastic growth, is employed by plants to cope with adverse environmental conditions. Ethylene is a key regulator of this process and, in Arabidopsis thaliana, hyponasty is induced by this phytohormone via promotion of epidermal cell expansion in a proximal zone of the abaxial side of the petiole. ROTUNDIFOLIA3/CYP90C1 encodes an enzyme which was shown to catalyse C-23 hydroxylation of several brassinosteroids (BRs) - phytohormones involved in, for example, organ growth, cell expansion, cell division, and responses to abiotic and biotic stresses. This study tested the interaction between ethylene and BRs in regulating hyponastic growth. A mutant isolated in a forward genetic screen, with reduced hyponastic response to ethylene treatment, was allelic to rot3. The cause of the reduced hyponastic growth in this mutant was examined by studying ethylene-BR interaction during local cell expansion, pharmacological inhibition of BR synthesis and ethylene effects on transcription of BR-related genes. This work demonstrates that rot3 mutants are impaired in local cell expansion driving hyponasty. Moreover, the inhibition of BR biosynthesis reduces ethylene-induced hyponastic growth and ethylene increases sensitivity to BR in promoting cell elongation in Arabidopsis hypocotyls. Together, the results show that ROT3 modulates ethylene-induced petiole movement and that this function is likely BR related.

Measuring the diurnal pattern of leaf hyponasty and growth in Arabidopsis - a novel phenotyping approach using laser scanning

Plants forming a rosette during their juvenile growth phase, such as Arabidopsis thaliana (L.) Heynh., are able to adjust the size, position and orientation of their leaves. These growth responses are under the control of the plants circadian clock and follow a characteristic diurnal rhythm. For instance, increased leaf elongation and hyponasty - defined here as the increase in leaf elevation angle - can be observed when plants are shaded. Shading can either be caused by a decrease in the fluence rate of photosynthetically active radiation (direct shade) or a decrease in the fluence rate of red compared with far-red radiation (neighbour detection). In this paper we report on a phenotyping approach based on laser scanning to measure the diurnal pattern of leaf hyponasty and increase in rosette size. In short days, leaves showed constitutively increased leaf elevation angles compared with long days, but the overall diurnal pattern and the magnitude of up and downward leaf movement was independent of daylength. Shade treatment led to elevated leaf angles during the first day of application, but did not affect the magnitude of up and downward leaf movement in the following day. Using our phenotyping device, individual plants can be non-invasively monitored during several days under different light conditions. Hence, it represents a proper tool to phenotype light- and circadian clock-mediated growth responses in order to better understand the underlying regulatory genetic network.

Plant neighbor detection through touching leaf tips precedes phytochrome signals

Plants in dense vegetation compete for resources, including light, and optimize their growth based on neighbor detection cues. The best studied of such behaviors is the shade-avoidance syndrome that positions leaves in optimally lit zones of a vegetation. Although proximate vegetation is known to be sensed through a reduced ratio between red and far-red light, we show here through computational modeling and manipulative experiments that leaves of the rosette species Arabidopsis thaliana first need to move upward to generate sufficient light reflection potential for subsequent occurrence and perception of a reduced red to far-red ratio. This early hyponastic leaf growth response is not induced by known neighbor detection cues under both climate chamber and natural sunlight conditions, and we identify a unique way for plants to detect future competitors through touching of leaf tips. This signal occurs before light signals and appears to be the earliest means of above-ground plant-plant signaling in horizontally growing rosette plants.

Haemoglobin modulates NO emission and hyponasty under hypoxia-related stress in Arabidopsis thaliana

Nitric oxide (NO) and ethylene are signalling molecules that are synthesized in response to oxygen depletion. Non-symbiotic plant haemoglobins (Hbs) have been demonstrated to act in roots under oxygen depletion to scavenge NO. Using Arabidopsis thaliana plants, the online emission of NO or ethylene was directly quantified under normoxia, hypoxia (0.1-1.0% O(2)), or full anoxia. The production of both gases was increased with reduced expression of either of the Hb genes GLB1 or GLB2, whereas NO emission decreased in plants overexpressing these genes. NO emission in plants with reduced Hb gene expression represented a major loss of nitrogen equivalent to 0.2mM nitrate per 24h under hypoxic conditions. Hb gene expression was greatly enhanced in flooded roots, suggesting induction by reduced oxygen diffusion. The function could be to limit loss of nitrogen under NO emission. NO reacts with thiols to form S-nitrosylated compounds, and it is demonstrated that hypoxia substantially increased the content of S-nitrosylated compounds. A parallel up-regulation of Hb gene expression in the normoxic shoots of the flooded plants may reflect signal transmission from root to shoot via ethylene and a role for Hb in the shoots. Hb gene expression was correlated with ethylene-induced upward leaf movement (hyponastic growth) but not with hypocotyl growth, which was Hb independent. Taken together the data suggest that Hb can influence flood-induced hyponasty via ethylene-dependent and, possibly, ethylene-independent pathways.

OSCILLATOR: A system for analysis of diurnal leaf growth using infrared photography combined with wavelet transformation

BACKGROUND

Quantification of leaf movement is an important tool for characterising the effects of environmental signals and the circadian clock on plant development. Analysis of leaf movement is currently restricted by the attachment of sensors to the plant or dependent upon visible light for time-lapse photography. The study of leaf growth movement rhythms in mature plants under biological relevant conditions, e.g. diurnal light and dark conditions, is therefore problematic.

RESULTS

Here we present OSCILLATOR, an affordable system for the analysis of rhythmic leaf growth movement in mature plants. The system contains three modules: (1) Infrared time-lapse imaging of growing mature plants (2) measurement of projected distances between leaf tip and plant apex (leaf tip tracking growth-curves) and (3) extraction of phase, period and amplitude of leaf growth oscillations using wavelet analysis. A proof-of-principle is provided by characterising parameters of rhythmic leaf growth movement of different Arabidopsis thaliana accessions as well as of Petunia hybrida and Solanum lycopersicum plants under diurnal conditions. The amplitude of leaf oscillations correlated to published data on leaf angles, while amplitude and leaf length did not correlate, suggesting a distinct leaf growth profile for each accession. Arabidopsis mutant accession Landsberg erecta displayed a late phase (timing of peak oscillation) compared to other accessions and this trait appears unrelated to the ERECTA locus.

CONCLUSIONS

OSCILLATOR is a low cost and easy to implement system that can accurately and reproducibly quantify rhythmic growth of mature plants for different species under diurnal light/dark cycling.