Interactions between ethylene and gibberellins in phytochrome-mediated shade avoidance responses in tobacco

Prolonged Post-Harvest Preservation in Lettuce (Lactuca sativa L.) by Reducing Water Loss Rate and Chlorophyll Degradation Regulated through Lighting Direction-Induced Morphophysiological Improvements

To investigate the relationship between the lighting direction-induced morphophysiological traits and post-harvest storage of lettuce, the effects of different lighting directions (top, T; top + side, TS; top + bottom, TB; side + bottom, SB; and top + side + bottom, TSB; the light from different directions for a sum of light intensity of 600 μmol·m-2·s-1 photosynthetic photon flux density (PPFD)) on the growth morphology, root development, leaf thickness, stomatal density, chlorophyll concentration, photosynthesis, and chlorophyll fluorescence, as well as the content of nutrition such as carbohydrates and soluble proteins in lettuce were analyzed. Subsequently, the changes in water loss rate, membrane permeability (measured as relative conductivity and malondialdehyde (MDA) content), brittleness (assessed by both brittleness index and β-galactosidase (β-GAL) activity), and yellowing degree (evaluated based on chlorophyll content, and activities of chlorophyllase (CLH) and pheophytinase (PPH)) were investigated during the storage after harvest. The findings indicate that the TS treatment can effectively reduce shoot height, increase crown width, enhance leaves' length, width, number, and thickness, and improve chlorophyll fluorescence characteristics, photosynthetic capacity, and nutrient content in lettuce before harvest. Specifically, lettuce's leaf thickness and stomatal density showed a significant increase. Reasonable regulation of water loss in post-harvested lettuce is essential for delaying chlorophyll degradation. It was utilized to mitigate the increase in conductivity and hinder the accumulation of MDA in lettuce. The softening speed of leafy vegetables was delayed by effectively regulating the activity of the β-GAL. Chlorophyll degradation was alleviated by affecting CLH and PPH activities. This provides a theoretical basis for investigating the relationship between creating a favorable light environment and enhancing the post-harvest preservation of leafy vegetables, thus prolonging their post-harvest storage period through optimization of their morphophysiological phenotypes.

Plant competition cues activate a singlet oxygen signaling pathway in Arabidopsis thaliana

Oxidative stress responses of Arabidopsis to reflected low red to far-red signals (R:FR ≈ 0.3) generated by neighboring weeds or an artificial source of FR light were compared with a weed-free control (R:FR ≈1.6). In the low R:FR treatments, induction of the shade avoidance responses (SAR) coincided with increased leaf production of singlet oxygen (1O2). This 1O2 increase was not due to protochlorophyllide accumulation and did not cause cell death. Chemical treatments, however, with 5-aminolevulinic acid (the precursor of tetrapyrrole biosynthesis) and glutathione (a quinone A reductant) enhanced cell death and growth inhibition. RNA sequencing revealed that transcriptome responses to the reflected low R:FR light treatments minimally resembled previously known Arabidopsis 1O2 generating systems that rapidly generate 1O2 following a dark to light transfer. The upregulation of only a few early 1O2 responsive genes (6 out of 1931) in the reflected low R:FR treatments suggested specificity of the 1O2 signaling. Moreover, increased expression of two enzyme genes, the SULFOTRANSFERASE ST2A (ST2a) and the early 1O2-responsive IAA-LEUCINE RESISTANCE (ILR)-LIKE6 (ILL6), which negatively regulate jasmonate level, suggested that repression of bioactive JAs may promote the shade avoidance (versus defense) and 1O2 acclimation (versus cell death) responses to neighboring weeds.

Attenuated total reflection Fourier-transform infrared spectroscopy reveals environment specific phenotypes in clonal Japanese knotweed

BACKGROUND

Japanese knotweed (Reynoutria japonica var. japonica), a problematic invasive species, has a wide geographical distribution. We have previously shown the potential for attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy and chemometrics to segregate regional differentiation between Japanese knotweed plants. However, the contribution of environment to spectral differences remains unclear. Herein, the response of Japanese knotweed to varied environmental habitats has been studied. Eight unique growth environments were created by manipulation of the red: far-red light ratio (R: FR), water availability, nitrogen, and micronutrients. Their impacts on plant growth, photosynthetic parameters, and ATR-FTIR spectral profiles, were explored using chemometric techniques, including principal component analysis (PCA), linear discriminant analysis, support vector machines (SVM) and partial least squares regression. Key wavenumbers responsible for spectral differences were identified with PCA loadings, and molecular biomarkers were assigned. Partial least squared regression (PLSR) of spectral absorbance and root water potential (RWP) data was used to create a predictive model for RWP.

RESULTS

Spectra from plants grown in different environments were differentiated using ATR-FTIR spectroscopy coupled with SVM. Biomarkers highlighted through PCA loadings corresponded to several molecules, most commonly cell wall carbohydrates, suggesting that these wavenumbers could be consistent indicators of plant stress across species. R: FR most affected the ATR-FTIR spectra of intact dried leaf material. PLSR prediction of root water potential achieved an R2 of 0.8, supporting the potential use of ATR-FTIR spectrometers as sensors for prediction of plant physiological parameters.

CONCLUSIONS

Japanese knotweed exhibits environmentally induced phenotypes, indicated by measurable differences in their ATR-FTIR spectra. This high environmental plasticity reflected by key biomolecular changes may contribute to its success as an invasive species. Light quality (R: FR) appears critical in defining the growth and spectral response to environment. Cross-species conservation of biomarkers suggest that they could function as indicators of plant-environment interactions including abiotic stress responses and plant health.

Organ-specific transcriptional regulation by HFR1 and HY5 in response to shade in Arabidopsis

Light is crucial for plants and serves as a signal for modulating their growth. Under shade, where red to far-red light ratio is low, plants exhibit shade avoidance responses (SAR). LONG HYPOCOTYL IN FAR-RED 1 (HFR1) and ELONGATED HYPOCOTYL 5 (HY5) are known to be negative regulators of SAR and physically interact with one another. However, transcriptional regulatory network underlying SAR by these two transcription factors has not been explored. Here, we performed organ-specific transcriptome analyses of Arabidopsis thaliana hfr1-5, hy5-215 and hfr1hy5 to identify genes that are co-regulated by HFR1 and HY5 in hypocotyls and cotyledons. Genes co-regulated by HFR1 and HY5 were enriched in various processes related to cell wall modification and chlorophyll biosynthesis in hypocotyls. Phytohormone (abscisic acid and jasmonic acid) and light responses were significantly regulated by HFR1 and HY5 in both organs, though it is more prominent under shade in cotyledons. HFR1 and HY5 also differentially regulate the expression of the cell wall-related genes for xyloglucan endotransglucosylase/hydrolase, expansin, arabinogalactan protein and class III peroxidase depending on the organs. Furthermore, HFR1 and HY5 cooperatively regulated hypocotyl responsiveness to shade through auxin metabolism. Together, our study illustrates the importance of the HFR1-HY5 module in regulating organ-specific shade responses in Arabidopsis.

Changes induced by parental neighboring touch in the clonal plant Glechoma longituba depend on the light environment

Introduction

Touch by neighboring plants is a common but overlooked environmental variable for plants, especially in dense vegetation. In addition, shade is inevitable for understory plants. The growth performance of clonal plant to the interaction between thigmomorphogenesis and shade response, and their impact on light adaptability is still unknown.

Methods

At the present study, parental ramets of Glechoma longituba were exposed to two conditions (neighboring touch and shade), and their offspring ramets were in ambient or shaded environment. The phenotype and growth of parental and offspring ramets were analyzed.

Results

The results showed that neighboring touch of parental ramets regulated the performance of offspring ramets, while the effect depended on the light environment. The parental neighboring touch occurring in ambient environment suppressed the expansion of leaf organ, showed as a shorter petiole and smaller leaf area. Moreover, G. longituba exhibited both shade avoidance and shade tolerance characters to shaded environment, such as increased leaf area ratio and leaf mass ratio, longer specific petiole length and specific stolon length. It was notable that these characters of shade response could be promoted by parental neighboring touch to some extent. Additionally, parental light environment plays an important role in offspring growth, parent with ambient light always had well-grown offspring whatever the light condition of offspring, but the growth of offspring whose parent in shaded environment was inhibited. Finally, for the offspring with shaded environment, the touch between parental ramets in shade environment showed a disadvantage on their growth, but the influence of the touch between parental ramets in ambient environment was slight.

Discussion

Overall, the interaction of parental neighboring touch and shade environment complicate the growth of understory plants, the performance of plants is the integrated effect of both. These findings are conducive to an in-depth understanding of the environmental adaptation of plants.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Cryptochromes suppress leaf senescence in response to blue light in Arabidopsis

The induction and progression of leaf senescence are effectively changed according to the light environment. The leaf senescence response is enhanced when plants are grown under a dense shade cast by neighboring vegetation. Although the fluence rate of the red and blue regions in the light spectrum is strongly attenuated under shade, photosensory mechanisms that underpin the blue light response are still unclear. In this study, we analyzed leaf senescence in response to blue light in Arabidopsis (Arabidopsis thaliana). We found that leaf senescence was promoted by the elimination of active phytochrome Pfr by pulsed far-red (FR) light, whereas irradiation with blue light suppressed leaf senescence in the wild type but not in the cryptochrome (CRY)-deficient mutant, cry1 cry2. Hence, two light-sensing modes contributed to the suppression of leaf senescence that was dependent on light spectrum features. First was the leaf senescence response to blue light, which was mediated exclusively by cryptochromes. Second was the phytochrome-mediated leaf senescence response to red/FR light. Physiological analysis of transgenic plants expressing green fluorescent protein (GFP)-tagged CRY2 revealed that photo-activation of cryptochromes was required to suppress leaf senescence in response to blue light. Transcriptomic analysis further uncovered the molecular and cellular processes involved in the regulation of leaf senescence downstream of cryptochromes. Furthermore, analysis of cryptochrome-downstream components indicated that ELONGATED HYPOCOTYL 5 (HY5) and PHYTOCHROME INTERACTING FACTOR (PIF) 4 and PIF5 were required for suppression and promotion of leaf senescence, respectively.

Effects of Monochromatic Light on Growth and Quality of Pistacia vera L

Light-emitting diodes (LEDs) are popular as a light source for in vitro plants because they save energy and allow the morphology of the plant to be altered. The purpose of this study was to show that switching from classical fluorescent light (FL) to LED light can have both beneficial and adverse effects. Pistacia vera plantlets were exposed to FL, monochromatic Blue LED light (B), monochromatic Red LED light (R), and a 1:1 mixture of both B and R (BR). R increased the total weight, shoot length, number of shoots ≥ 1 cm, and proliferation. It also reduced hyperhydricity (HH), but also dramatically increased shoot tip necrosis (STN) and leaf necrosis (LN). B cured plants of HH and STN, but hardly enabled proliferation. It did not solve the problem of LN, but the plants were high in total chlorophyll and carotenoids. BR reduced HH but enabled limited proliferation, high STN, and LN. All three LED treatments reduced HH compared to FL. B induced both high total phenolic and flavonoid content and high DPPH-scavenging activity. These results show that switching from FL to LED can have a significant positive or negative effect on proliferation and quality. This suggests that finding an optimal lighting regimen will take a lot of trial and error.

LONG HYPOCOTYL IN FAR-RED 1 mediates a trade-off between growth and defense under shade in Arabidopsis

Plants respond to vegetative shade with developmental and physiological changes that is collectively known as shade avoidance syndrome (SAS). Although LONG HYPOCOTYL IN FAR-RED 1 (HFR1) is known to be a negative regulator of SAS by forming heterodimers with other basic helix-loop-helix (bHLH) transcription factors to inhibit them, its function in genome-wide transcriptional regulation is not fully elucidated. Here, we performed RNA-sequencing analyses of hfr1-5 and HFR1 overexpression line (HFR1(ΔN)-OE) to comprehensively identify HFR1-regulated genes at different time points of shade treatment. We found that HFR1 mediates the trade-off between shade-induced growth and shade-repressed defense, by regulating the expression of relevant genes in shade. Genes involved in promoting growth, such as for auxin biosynthesis, transport, signaling and response were induced by shade but suppressed by HFR1 at both short and long durations of shade. Likewise, most ethylene-related genes were shade-induced and HFR1-repressed. On the other hand, shade suppressed defense-related genes while HFR1 induced their expression, especially under long duration of shade treatment. We demonstrated that HFR1 confers increased resistance to bacterial infection under shade.

Elucidation of the interactome of the sucrose transporter StSUT4: sucrose transport is connected to ethylene and calcium signalling

Sucrose transporters of the SUT4 clade show dual targeting to both the plasma membrane as well as to the vacuole. Previous investigations revealed a role for the potato sucrose transporter StSUT4 in flowering, tuberization, shade avoidance response, and ethylene production. Down-regulation of StSUT4 expression leads to early flowering, tuberization under long days, far-red light insensitivity, and reduced diurnal ethylene production. Sucrose export from leaves was increased and a phase-shift of soluble sugar accumulation in source leaves was observed, arguing for StSUT4 to be involved in the entrainment of the circadian clock. Here, we show that StSUT4, whose transcripts are highly unstable and tightly controlled at the post-transcriptional level, connects components of the ethylene and calcium signalling pathway. Elucidation of the StSUT4 interactome using the split ubiquitin system helped to prove direct physical interaction between the sucrose transporter and the ethylene receptor ETR2, as well as with the calcium binding potato calmodulin-1 (PCM1) protein, and a calcium-load activated calcium channel. The impact of calcium ions on transport activity and dual targeting of the transporter was investigated in detail. For this purpose, a reliable esculin-based transport assay was established for SUT4-like transporters. Site-directed mutagenesis helped to identify a diacidic motif within the seventh transmembrane spanning domain that is essential for sucrose transport activity and targeting, but not required for calcium-dependent inhibition. A link between sucrose, calcium and ethylene signalling has been previously postulated with respect to pollen tube growth, shade avoidance response, or entrainment of the circadian clock. Here, we provide experimental evidence for the direct interconnection of these signalling pathways at the molecular level by direct physical interaction of the main players.

Subcellular dynamics and protein-protein interactions of plant sucrose transporters

Although extensively studied for their role in long distance transport, plant sucrose transporters are active not only in the phloem but throughout the plant body. Sucrose transporters of the SUT family were first described to be plasma membrane-resident proteins, but recent investigations revealed that subcellular dynamics of these transporters were part of complex regulatory mechanisms. The yeast two-hybrid split-ubiquitin system, tandem-affinity purification, and bimolecular-fluorescence complementation aided in identification of a complex network of SUT-interacting proteins that led to answers to many open questions. We found, for example, interacting proteins localized to other subcellular compartments. Although sucrose transporters were assumed to be localized mainly on the plasma membrane, and the tonoplast in the case of SUT4, the interaction partners were not exclusively predicted to be plasma membrane proteins, but belonged to the extracellular space (cell wall), intracellular vesicles, the ER, tonoplast, nuclei, and peroxisomes, among other cellular compartments. A subset of the SUT-interacting proteins localized exclusively to plasmodesmata. We conclude that (transient) protein-protein interactions of integral membrane proteins help to sequester SUTs to subcellular compartments, such as membrane microdomains, with specific functions to enable subcellular transport and cell-to-cell trafficking via plasmodesmata. Identification of SNARE proteins (soluble N-ethylmaleimide-sensitive factor protein attachment protein receptors) and protein disulfide isomerases support the assumption that the protein-protein interaction plays an important role for the subcellular movement of sugar transporters. It becomes apparent that the interaction partners provide a substantial impact on how and where the transporter is localized or processed for either targeting to a specific cellular or extracellular location, or tagging for degradation or recycling. In this review, interacting proteins, as well as the role of oligomeric complex formation, post-translational modification, and stress responses are summarized for SUTs of higher plants.

Lighting from Top and Side Enhances Photosynthesis and Plant Performance by Improving Light Usage Efficiency

Light is a critical environmental factor that influences plant growth and development, ranging from seed germination to flowering and fruiting. This study was carried out to explore how the optimal combination of various lighting directions increases the light usage efficiency and influences the plant morphophysiology, by investigating the plant growth parameters, leaf anatomy, epidermal morphology, stomatal properties, chlorophyll content, key physiological changes, and correlated gene expressions. In closed-type plant growth chambers, rooted cuttings of two chrysanthemum (Chrysanthemum morifolium Ramat.) cultivars, “Pearl Egg” and “Gaya Glory”, were subjected to a 10-h photoperiod with 600 μmol∙m⁻²·s⁻¹ photosynthetic photon flux density (PPFD) provided by light-emitting diodes (LEDs) in each light-direction combination (top (1/1) (T), top (1/2) + side (1/2) (TS), top (1/2) + bottom (1/2) (TB), side (1/2) + bottom (1/2) (SB), and top (1/3) + side (1/3) + bottom (1/3) (TSB)). The TS lighting significantly enhanced the morphophysiological performance, compared to the other lighting direction combinations. Notably, the excellent branch formation and earlier flowering were induced by the TS lighting in both “Pearl Egg” and “Gaya Glory” plants.

Side Lighting Enhances Morphophysiology by Inducing More Branching and Flowering in Chrysanthemum Grown in Controlled Environment

Light is one of the most important factors that influence plant growth and development. This study was conducted to examine how lighting direction affects plant morphophysiology by investigating plant growth parameters, leaf anatomy, epidermal cell elongation, stomatal properties, chloroplast arrangement, and physiological changes. In closed-type plant factory units, the rooted cuttings of two chrysanthemum (Chrysanthemum morifolium Ramat.) cultivars, ‘Gaya Glory’ and ‘Pearl Egg’, were subjected to a 10 h photoperiod with a 300 μmol∙m⁻²∙s⁻¹ photosynthetic photon flux density (PPFD) provided by light-emitting diodes (LEDs) from three directions relative to the plant including the top, side, and bottom. Compared to the top or bottom lighting, the side lighting greatly enhanced the plant growth, improved the leaf internal structure and chloroplast arrangement, induced small stomata with a higher density, and promoted stomatal opening, which is associated with an increased stomatal conductance and photosynthetic efficiency. It is worth noting that the side lighting significantly enhanced the induction of branching and flowering for both cultivars., The plants grown with side lighting consistently exhibited the greatest physiological performance. We conclude that the lighting direction had a profound effect on the morphophysiological characteristics of chrysanthemum, and that side lighting dramatically promoted their growth and development, especially in their branching and flowering.

ABA and Bud Dormancy in Perennials: Current Knowledge and Future Perspective

Bud dormancy is an evolved trait that confers adaptation to harsh environments, and affects flower differentiation, crop yield and vegetative growth in perennials. ABA is a stress hormone and a major regulator of dormancy. Although the physiology of bud dormancy is complex, several advancements have been achieved in this field recently by using genetics, omics and bioinformatics methods. Here, we review the current knowledge on the role of ABA and environmental signals, as well as the interplay of other hormones and sucrose, in the regulation of this process. We also discuss emerging potential mechanisms in this physiological process, including epigenetic regulation.

Understanding a Mechanistic Basis of ABA Involvement in Plant Adaptation to Soil Flooding: The Current Standing

Soil flooding severely impairs agricultural crop production. Plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by the elaborated hormonal signaling network. The most prominent of these hormones is ethylene, which has been firmly established as a critical signal in flooding tolerance. ABA (abscisic acid) is also known as a “stress hormone” that modulates various responses to abiotic stresses; however, its role in flooding tolerance remains much less established. Here, we discuss the progress made in the elucidation of morphological adaptations regulated by ABA and its crosstalk with other phytohormones under flooding conditions in model plants and agriculturally important crops.

Physiological and metabolic bases of increased growth in the tomato ethylene-insensitive mutant Never ripe: extending ethylene signaling functions

The tomato mutant Never ripe (Nr), a loss-of-function for the ethylene receptor SlETR3, shows enhanced growth, associated with increased carbon assimilation and a rewiring of the central metabolism. Compelling evidence has demonstrated the importance of ethylene during tomato fruit development, yet its role on leaf central metabolism and plant growth remains elusive. Here, we performed a detailed characterization of Never ripe (Nr) tomato, a loss-of-function mutant for the ethylene receptor SlETR3, known for its fruits which never ripe. However, besides fruits, the Nr gene is also constitutively expressed in vegetative tissues. Nr mutant showed a growth enhancement during both the vegetative and reproductive stage, without an earlier onset of leaf senescence, with Nr plants exhibiting a higher number of leaves and an increased dry weight of leaves, stems, roots, and fruits. At metabolic level, Nr also plays a significant role with the mutant showing changes in carbon assimilation, carbohydrates turnover, and an exquisite reprogramming of a large number of metabolite levels. Notably, the expression of genes related to ethylene signaling and biosynthesis are not altered in Nr. We assess our results in the context of those previously published for tomato fruits and of current models of ethylene signal transduction, and conclude that ethylene insensitivity mediated by Nr impacts the whole central metabolism at vegetative stage, leading to increased growth rates.

Global trends in phenotypic plasticity of plants

Predicting plastic responses is crucial to assess plant species potential to adapt to climate change, but little is known about which factors drive the biogeographical patterns of phenotypic plasticity in plants. Theory predicts that climatic variability would select for increased phenotypic plasticity, whereas evidence indicates that stressful conditions can limit phenotypic plasticity. Using a meta-analytic, phylogeny-corrected approach to global data on plant phenotypic plasticity, we tested whether latitude, climate, climatic variability and/or stressful conditions are predictors of plastic responses at a biogeographical scale. We found support for a positive association between phenotypic plasticity and climatic variability only for plasticity in allocation. Plasticity in leaf morphology, size and physiology were positively associated with mean annual temperature. We also found evidence that phenotypic plasticity in physiology is limited by cold stress. Overall, plant plastic responses to non-climatic factors were stronger than responses to climatic factors. However, while climatic conditions were associated with plant plastic responses to climatic factors, they generally did not relate to plastic responses to other abiotic or biotic factors. Our study highlights the need to consider those factors that favour and limit phenotypic plasticity in order to improve predictive frameworks addressing plant species' potential to adapt to climate change.

Integration of light and hormone signaling pathways in the regulation of plant shade avoidance syndrome

As sessile organisms, plants are unable to move or escape from their neighboring competitors under high-density planting conditions. Instead, they have evolved the ability to sense changes in light quantity and quality (such as a reduction in photoactive radiation and drop in red/far-red light ratios) and evoke a suite of adaptative responses (such as stem elongation, reduced branching, hyponastic leaf orientation, early flowering and accelerated senescence) collectively termed shade avoidance syndrome (SAS). Over the past few decades, much progress has been made in identifying the various photoreceptor systems and light signaling components implicated in regulating SAS, and in elucidating the underlying molecular mechanisms, based on extensive molecular genetic studies with the model dicotyledonous plant Arabidopsis thaliana. Moreover, an emerging synthesis of the field is that light signaling integrates with the signaling pathways of various phytohormones to coordinately regulate different aspects of SAS. In this review, we present a brief summary of the various cross-talks between light and hormone signaling in regulating SAS. We also present a perspective of manipulating SAS to tailor crop architecture for breeding high-density tolerant crop cultivars.

Light signalling shapes plant-plant interactions in dense canopies

Plants growing at high densities interact via a multitude of pathways. Here, we provide an overview of mechanisms and functional consequences of plant architectural responses initiated by light cues that occur in dense vegetation. We will review the current state of knowledge about shade avoidance, as well as its possible applications. On an individual level, plants perceive neighbour-associated changes in light quality and quantity mainly with phytochromes for red and far-red light and cryptochromes and phototropins for blue light. Downstream of these photoreceptors, elaborate signalling and integration takes place with the PHYTOCHROME INTERACTING FACTORS, several hormones and other regulators. This signalling leads to the shade avoidance responses, consisting of hyponasty, stem and petiole elongation, apical dominance and life cycle adjustments. Architectural changes of the individual plant have consequences for the plant community, affecting canopy structure, species composition and population fitness. In this context, we highlight the ecological, evolutionary and agricultural importance of shade avoidance.

High planting density induces the expression of GA3-oxidase in leaves and GA mediated stem elongation in bioenergy sorghum

The stems of bioenergy sorghum hybrids at harvest are > 4 m long, contain > 40 internodes and account for ~ 80% of harvested biomass. In this study, bioenergy sorghum hybrids were grown at four planting densities (~ 20,000 to 132,000 plants/ha) under field conditions for 60 days to investigate the impact shading has on stem growth and biomass accumulation. Increased planting density induced a > 2-fold increase in sorghum internode length and a ~ 22% decrease in stem diameter, a typical shade avoidance response. Shade-induced internode elongation was due to an increase in cell length and number of cells spanning the length of internodes. SbGA3ox2 (Sobic.003G045900), a gene encoding the last step in GA biosynthesis, was expressed ~ 20-fold higher in leaf collar tissue of developing phytomers in plants grown at high vs. low density. Application of GA3 to bioenergy sorghum increased plant height, stem internode length, cell length and the number of cells spanning internodes. Prior research showed that sorghum plants lacking phytochrome B, a key photoreceptor involved in shade signaling, accumulated more GA1 and displayed shade avoidance phenotypes. These results are consistent with the hypothesis that increasing planting density induces expression of GA3-oxidase in leaf collar tissue, increasing synthesis of GA that stimulates internode elongation.

Bryophytes can recognize their neighbours through volatile organic compounds

Communication between vascular plants through volatile organic compounds (VOCs) impacts on ecosystem functioning. However, nothing is known about that between non-vascular plants. To investigate plant-plant VOCs interaction in bryophytes we exposed rare peatland moss Hamatocaulis vernicosus to VOCs of its common competitor Sphagnum flexuosum in an air-flow system of connected containers under artificial light, supplemented or unsupplemented by far-red (FR) light. When exposed to VOCs of S. flexuosum, shoots of H. vernicosus elongated and emitted six times higher amounts of a compound chemically related to β-cyclocitral, which is employed in stress signalling and allelopathy in vascular plants. The VOCs emission was affected similarly by FR light addition, possibly simulating competition stress. This is the first evidence of plant-plant VOCs interaction in non-vascular plants, analogous to that in vascular plants. The findings open new possibilities for understanding the language and evolution of communication in land plants.

Progress of Research on the Regulatory Pathway of the Plant Shade-Avoidance Syndrome

When subject to vegetational shading, shade-avoiding plants detect neighbors by perceiving reduced light quantity and altered light quality. The former includes decreases in the ratio of red to far-red wavelengths (low R:FR) and low blue light ratio (LBL) predominantly detected by phytochromes and cryptochromes, respectively. By integrating multiple signals, plants generate a suite of responses, such as elongation of a variety of organs, accelerated flowering, and reduced branching, which are collectively termed the shade-avoidance syndrome (SAS). To trigger the SAS, interactions between photoreceptors and phytochrome-interacting factors are the general switch for activation of downstream signaling pathways. A number of transcription factor families and phytohormones, especially auxin, gibberellins, ethylene, and brassinosteroids, are involved in the SAS processes. In this review, shade signals, the major photoreceptors involved, and the phenotypic characteristics of the shade-intolerant plant Arabidopsis thaliana are described in detail. In addition, integration of the signaling mechanisms that link photoreceptors with multiple hormone signaling pathways is presented and future research directions are discussed.

Gibberellin Signaling Is Required for Far-Red Light-Induced Shoot Elongation in Pinus tabuliformis Seedlings

Gibberellin (GA) is known to play an important role in low red/far-red (R:FR) light ratio-mediated hypocotyl and petiole elongation in Arabidopsis (Arabidopsis thaliana). However, the regulatory relationship between low R:FR and GAs remains unclear, especially in gymnosperms. To increase our understanding of the molecular basis of low R:FR-mediated shoot elongation in pines and to determine whether there is an association between low R:FR and GAs action, we explored the morphological and transcriptomic changes triggered by low R:FR, GAs, and paclobutrazol (PAC), a GAs biosynthesis inhibitor, in Pinus tabuliformis seedlings. Transcriptome profiles revealed that low R:FR conditions and GAs have a common set of transcriptional targets in P. tabuliformis We provide evidence that the effect of low R:FR on shoot elongation in P. tabuliformis is at least partially modulated by GAs accumulation, which can be largely attenuated by PAC. GAs are also involved in the cross talk between different phytohormones in the low R:FR response. A GA biosynthesis gene, encoding ent-kaurenoic acid oxidase (KAO), was strongly stimulated by low R:FR without being affected by GAs feedback regulation or the photoperiod. We show that GA signaling is required for low R:FR-induced shoot elongation in P tabuliformis seedlings, and that there are different regulatory targets for low R:FR-mediated GA biosynthesis between conifers and angiosperms.

Combating Spring Frost With Ethylene

The sustainable fruit production in temperate and boreal regions is often imperiled by spring frosts. The risk of frost damage and the resulting economic losses have been increasing in the recent years as a result of the global climate change. Among the many approaches in mitigating frost damages, an ethylene-based compound, ethephon has proven to be effective in delaying bloom time in many fruit species and, thereby, avoid frost damage. However, effective concentrations of ethephon are often associated with harmful effects on fruit trees, which largely limit its use. Relatively, limited research attention has been given to understand the mechanisms underlying this ethylene-mediated bloom delay, thus hindering the progress in exploring its potential in frost protection. Recent advances in omics and bioinformatics have facilitated the identification of critical molecular and biochemical pathways that govern the progression of bud dormancy in deciduous woody perennials. In this review, we summarized our current understanding of the function of ethylene and its interaction with other networks in modulating dormancy and blooming in temperate fruit trees. Some possible mechanisms are also proposed that might potentially guide future studies attempting to decipher the dormancy regulation or searching for methods to alleviate frost damages.

Physiological and Transcriptomic Analyses Elucidate That Exogenous Calcium Can Relieve Injuries to Potato Plants (Solanum tuberosum L.) under Weak Light

Light is one of the most important abiotic factors for most plants, which affects almost all growth and development stages. In this study, physiological indicators suggest that the application of exogenous Ca2+ improves photosynthesis and changes phytohormone levels. Under weak light, photosynthetic parameters of the net photosynthetic rate (PN), stomatal conductance (Gs), and transpiration rate (Tr) decreased; the antioxidation systems peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) reduced; the degrees of malondialdehyde (MDA), H2O2, and superoxide anion (O2-) free radical damage increased; while exogenous Ca2+ treatment was significantly improved. RNA-seq analysis indicated that a total of 13,640 differently expressed genes (DEGs) were identified and 97 key DEGs related to hormone, photosynthesis, and calcium regulation were differently transcribed. Gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses, plant hormone signal transduction, photosynthesis, carbon metabolism, and phenylpropanoid biosynthesis were significantly enriched. Additionally, quantitative real-time PCR (qRT-PCR) analysis confirmed some of the key gene functions in response to Ca2+. Overall, these results provide novel insights into the complexity of Ca2+ to relieve injuries under weak light, and they are helpful for potato cultivation under weak light stress.

Light-induced stabilization of ACS contributes to hypocotyl elongation during the dark-to-light transition in Arabidopsis seedlings

Hypocotyl growth during seedling emergence is a crucial developmental transition influenced by light and phytohormones such as ethylene. Ethylene and light antagonistically control hypocotyl growth in either continuous light or darkness. However, how ethylene and light regulate hypocotyl growth, including seedling emergence, during the dark-to-light transition remains elusive. Here, we show that ethylene and light cooperatively stimulate a transient increase in hypocotyl growth during the dark-to-light transition via the light-mediated stabilization of 1-aminocyclopropane-1-carboxylic acid (ACC) synthases (ACSs), the rate-limiting enzymes in ethylene biosynthesis. We found that, in contrast to the known inhibitory role of light in hypocotyl growth, light treatment transiently increases hypocotyl growth in wild-type etiolated seedlings. Moreover, ACC, the direct precursor of ethylene, accentuates the effects of light on hypocotyl elongation during the dark-to-light transition. We determined that light leads to the transient elongation of hypocotyls by stabilizing the ACS5 protein during the dark-to-light transition. Furthermore, biochemical analysis of an ACS5 mutant protein bearing an alteration in the C-terminus indicated that light stabilizes ACS5 by inhibiting the degradation mechanism that acts through the C-terminus of ACS5. Our study reveals that plants regulate hypocotyl elongation during seedling establishment by coordinating light-induced ethylene biosynthesis at the post-translational level. Moreover, the stimulatory role of light on hypocotyl growth during the dark-to-light transition provides additional insights into the known inhibitory role of light in hypocotyl development.

Genetic Regulation of Ethylene Dosage for Cucumber Fruit Elongation

Plant organ growth and development are determined by a subtle balance between growth stimulation and inhibition. Fruit size and shape are important quality traits influencing yield and market value; however, the underlying mechanism regulating the balance of fruit growth to achieve final size and shape is not well understood. Here, we report a mechanistic model that governs cucumber (Cucumis sativus) fruit elongation through fine-tuning of ethylene homeostasis. We identified a cucumber mutant that bears short fruits owing to repressed cell division. SF1 (Short Fruit 1) encodes a cucurbit-specific RING-type E3 ligase, and the mutation resulted in its enhanced self-ubiquitination and degradation, but accumulation of ACS2 (1-aminocyclopropane-1-carboxylate synthase 2), a rate-limiting enzyme for ethylene biosynthesis. The overproduction of ethylene contributes to the short-fruit phenotype of sf1 Dysfunction of ACS2 resulted in reduced ethylene production, but still repressed cell division and shorter fruit, suggesting that ethylene is still required for basal fruit elongation. SF1 ubiquitinates and degrades both itself and ACS2 to control ethylene synthesis for dose-dependent effect on cell division and fruit elongation. Our findings reveal the mechanism by which ethylene dosage is regulated for the control of cell division in developing fruit.

Assessing Global DNA Methylation Changes Associated with Plasticity in Seven Highly Inbred Lines of Snapdragon Plants (Antirrhinum majus)

Genetic and epigenetic variations are commonly known to underlie phenotypic plastic responses to environmental cues. However, the role of epigenetic variation in plastic responses harboring ecological significance in nature remains to be assessed. The shade avoidance response (SAR) of plants is one of the most prevalent examples of phenotypic plasticity. It is a phenotypic syndrome including stem elongation and multiple other traits. Its ecological significance is widely acknowledged, and it can be adaptive in the presence of competition for light. Underlying genes and pathways were identified, but evidence for its epigenetic basis remains scarce. We used a proven and accessible approach at the population level and compared global DNA methylation between plants exposed to regular light and three different magnitudes of shade in seven highly inbred lines of snapdragon plants (Antirrhinum majus) grown in a greenhouse. Our results brought evidence of a strong SAR syndrome for which magnitude did not vary between lines. They also brought evidence that its magnitude was not associated with the global DNA methylation percentage for five of the six traits under study. The magnitude of stem elongation was significantly associated with global DNA demethylation. We discuss the limits of this approach and why caution must be taken with such results. In-depth approaches at the DNA sequence level will be necessary to better understand the molecular basis of the SAR syndrome.

The Influence of Light Intensity and Leaf Movement on Photosynthesis Characteristics and Carbon Balance of Soybean

In intercropping systems shading conditions significantly impair the seed yield and quality of soybean, and rarely someone investigated the minimum amount of light requirement for soybean growth and development. Therefore, it is an urgent need to determine the threshold light intensity to ensure sustainable soybean production under these systems. An integrated approach combining morphology, physiology, biochemistry and genetic analysis was undertaken to study the light intensity effects on soybean growth and development. A pot experiment was set up in a growth chamber under increasing light intensity treatments of 100 (L100), 200 (L200), 300 (L300), 400 (L400), and 500 (L500) μmol m-2 s-1. Compared with L100, plant height, hypocotyl length, and abaxial leaf petiole angle were decreased, biomass, root:shoot ratio, and stem diameter were increased, extremum was almost observed in L400 and L500. Leaf petiole movement and leaf hyponasty in each treatment has presented a tendency to decrease the leaf angle from L500 to L100. In addition, the cytochrome content (Chl a, Chl b, Car), net photosynthetic rate, chlorophyll fluorescence values of F v/F m, F v ' / F m ' , ETR, ΦPSII, and qP were increased as the light intensity increased, and higher values were noted under L400. Leaf microstructure and chloroplast ultrastructure positively improved with increasing light intensity, and leaf-thickness, palisade, and spongy tissues-thickness were increased by 105, 90, and 370%, under L500 than L100. Moreover, the cross-sectional area of chloroplast (C) outer membrane and starch grains (S), and sectional area ratio (S:C) was highest under L400 and L500, respectively. Compared to L100, the content of starch granules increased by 35.5, 122.0, 157.6, and 145.5%, respectively in L400. The same trends were observed in the enzyme activity of sucrose-synthase, sucrose phosphate synthase, starch synthase, rubisco, phosphoenol pyruvate carboxykinase, and phosphoenol pyruvate phosphatase. Furthermore, sucrose synthesis-related genes were also up-regulated by increasing light intensity, and the highest seed yield and yield related parameters were recorded in the L400. Overall, these results suggested that 400 and 500 μmol m-2 s-1 is the optimum light intensity which positively changed the leaf orientation and adjusts leaf angle to perpendicular to coming light, consequently, soybean plants grow well under prevailing conditions.

Hormonal Orchestration of Bud Dormancy Cycle in Deciduous Woody Perennials

Woody perennials enter seasonal dormancy to avoid unfavorable environmental conditions. Plant hormones are the critical mediators regulating this complex process, which is subject to the influence of many internal and external factors. Over the last two decades, our knowledge of hormone-mediated dormancy has increased considerably, primarily due to advancements in molecular biology, omics, and bioinformatics. These advancements have enabled the elucidation of several aspects of hormonal regulation associated with bud dormancy in various deciduous tree species. Plant hormones interact with each other extensively in a context-dependent manner. The dormancy-associated MADS (DAM) transcription factors appear to enable hormones and other internal signals associated with the transition between different phases of bud dormancy. These proteins likely hold a great potential in deciphering the underlying mechanisms of dormancy initiation, maintenance, and release. In this review, a recent understanding of the roles of plant hormones, their cross talks, and their potential interactions with DAM proteins during dormancy is discussed.

Auxin Contributes to the Intraorgan Regulation of Gene Expression in Response to Shade

Plants sense and respond to light via multiple photoreceptors including phytochrome. The decreased ratio of red to far-red light that occurs under a canopy triggers shade-avoidance responses, which allow plants to compete with neighboring plants. The leaf acts as a photoperceptive organ in this response. In this study, we investigated how the shade stimulus is spatially processed within the cotyledon. We performed transcriptome analysis on microtissue samples collected from vascular and nonvascular regions of Arabidopsis (Arabidopsis thaliana) cotyledons. In addition, we mechanically isolated and analyzed the vascular tissue. More genes were up-regulated by the shade stimulus in vascular tissues than in mesophyll and epidermal tissues. The genes up-regulated in the vasculature were functionally divergent and included many auxin-responsive genes, suggesting that various physiological/developmental processes might be controlled by shade stimulus in the vasculature. We then investigated the spatial regulation of these genes in the vascular tissues. A small vascular region within a cotyledon was irradiated with far-red light, and the response was compared with that when the whole seedling was irradiated with far-red light. Most of the auxin-responsive genes were not fully induced by the local irradiation, suggesting that perception of the shade stimulus requires that a wider area be exposed to far-red light or that a certain position in the mesophyll and epidermis of the cotyledon be irradiated. This result was consistent with a previous report that auxin synthesis genes are up-regulated in the periphery of the cotyledon. Hence, auxin acts as an important intraorgan signaling factor that controls the vascular shade response within the cotyledon.

Light, Ethylene and Auxin Signaling Interaction Regulates Carotenoid Biosynthesis During Tomato Fruit Ripening

Light signaling and plant hormones, particularly ethylene and auxins, have been identified as important regulators of carotenoid biosynthesis during tomato fruit ripening. However, whether and how the light and hormonal signaling cascades crosstalk to control this metabolic route remain poorly elucidated. Here, the potential involvement of ethylene and auxins in the light-mediated regulation of tomato fruit carotenogenesis was investigated by comparing the impacts of light treatments and the light-hyperresponsive high pigment-2 (hp2) mutation on both carotenoid synthesis and hormonal signaling. Under either light or dark conditions, the overaccumulation of carotenoids in hp2 ripening fruits was associated with disturbed ethylene production, increased expression of genes encoding master regulators of ripening and higher ethylene sensitivity and signaling output. The increased ethylene sensitivity observed in hp2 fruits was associated with the differential expression of genes encoding ethylene receptors and downstream signaling transduction elements, including the downregulation of the transcription factor ETHYLENE RESPONSE FACTOR.E4, a repressor of carotenoid synthesis. Accordingly, treatments with exogenous ethylene promoted carotenoid biosynthetic genes more intensively in hp2 than in wild-type fruits. Moreover, the loss of HP2 function drastically altered auxin signaling in tomato fruits, resulting in higher activation of the auxin-responsive promoter DR5, severe down-regulation of AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes and altered accumulation of AUXIN RESPONSE FACTOR (ARF) transcripts. Both tomato ARF2 paralogues (Sl-ARF2a and SlARF2b) were up-regulated in hp2 fruits, which agrees with the promotive roles played by these ARFs in tomato fruit ripening and carotenoid biosynthesis. Among the genes differentially expressed in hp2 fruits, the additive effect of light treatment and loss of HP2 function was particularly evident for those encoding carotenoid biosynthetic enzymes, ethylene-related transcription factors, Aux/IAAs and ARFs. Altogether, the data uncover the involvement of ethylene and auxin as part of the light signaling cascades controlling tomato fruit metabolism and provide a new link between light signaling, plant hormone sensitivity and carotenoid metabolism in ripening fruits.

Decision-making in plants under competition

Plants can plastically respond to light competition in three strategies, comprising vertical growth, which promotes competitive dominance; shade tolerance, which maximises performance under shade; or lateral growth, which offers avoidance of competition. Here, we test the hypothesis that plants can 'choose' between these responses, according to their abilities to competitively overcome their neighbours. We study this hypothesis in the clonal plant Potentilla reptans using an experimental setup that simulates both the height and density of neighbours, thus presenting plants with different light-competition scenarios. Potentilla reptans ramets exhibit the highest vertical growth under simulated short-dense neighbours, highest specific leaf area (leaf area/dry mass) under tall-dense neighbours, and tend to increase total stolon length under tall-sparse neighbours. These responses suggest shifts between 'confrontational' vertical growth, shade tolerance and lateral-avoidance, respectively, and provide evidence that plants adopt one of several alternative plastic responses in a way that optimally corresponds to prevailing light-competition scenarios.

The shade-avoidance syndrome: multiple signals and ecological consequences

Plants use photoreceptor proteins to detect the proximity of other plants and to activate adaptive responses. Of these photoreceptors, phytochrome B (phyB), which is sensitive to changes in the red (R) to far-red (FR) ratio of sunlight, is the one that has been studied in greatest detail. The molecular connections between the proximity signal (low R:FR) and a model physiological response (increased elongation growth) have now been mapped in considerable detail in Arabidopsis seedlings. We briefly review our current understanding of these connections and discuss recent progress in establishing the roles of other photoreceptors in regulating growth-related pathways in response to competition cues. We also consider processes other than elongation that are controlled by photoreceptors and contribute to plant fitness under variable light conditions, including photoresponses that optimize the utilization of soil resources. In examining recent advances in the field, we highlight emerging roles of phyB as a major modulator of hormones related to plant immunity, in particular salicylic acid and jasmonic acid (JA). Recent attempts to manipulate connections between light signals and defence in Arabidopsis suggest that it might be possible to improve crop health at high planting densities by targeting links between phyB and JA signalling.

Reducing shade avoidance responses in a cereal crop

Several researchers have hypothesized that shade avoidance behaviour is favoured by natural selection because it increases the fitness of individuals. Shade avoidance can be disadvantageous for crops, however, because it reduces allocation of resources to reproductive yield, increases the risk of lodging and reduces weed suppression. One approach to develop varieties with reduced shade avoidance and enhanced agronomic performance is by inducing mutations followed by phenotypic screening. We treated spring wheat seeds with ethyl methanesulfonate and screened the seedlings repeatedly under green filters for plants showing reduced elongation of the first leaf sheath and second leaf lamina. The shade avoidance responses of five promising mutant lines were further compared to non-mutated plants in a climate chamber experiment with added far-red light. Two of the selected lines displayed significantly reduced elongation under all light treatments while two lines showed reduced elongation only in added far-red light. The most promising mutant line did not differ in height from the non-mutated cultivar in neutral light, but elongated 20.6% less in strong far-red light. This traditional forward approach of screening mutagenized spring wheat produced plants with reduced shade avoidance responses. These mutants may generate new molecular handles to modify the reaction of plants to changes in light spectral distribution in traditional and novel cultivation systems.

Functional specialization of Nicotiana attenuata phytochromes in leaf development and flowering time

Phytochromes mainly function in photoautotrophic organisms to adjust growth in response to fluctuating light signals. The different isoforms of plant phytochromes often display both conserved and divergent roles, presumably to fine-tune plant responses to environmental signals and optimize fitness. Here we describe the distinct, yet partially redundant, roles of phytochromes NaPHYA, NaPHYB1 and NaPHYB2 in a wild tobacco species, Nicotiana attenuata using RNAi-silenced phytochrome lines. Consistent with results reported from other species, silencing the expression of NaPHYA or NaPHYB2 in N. attenuata had mild or no influence on plant development as long as NaPHYB1 was functional; whereas silencing the expression of NaPHYB1 alone strongly altered flowering time and leaf morphology. The contribution of NaPHYB2 became significant only in the absence of NaPHYB1; plants silenced for both NaPHYB1 and NaPHYB2 largely skipped the rosette-stage of growth to rapidly produce long, slender stalks that bore flowers early: hallmarks of the shade-avoidance responses. The phenotyping of phytochrome-silenced lines, combined with sequence and transcript accumulation analysis, suggest the independent functional diversification of the phytochromes, and a dominant role of NaPHYB1 and NaPHYB2 in N. attenuata's vegetative and reproductive development.

Hormonal Regulation in Shade Avoidance

At high vegetation density, shade-intolerant plants sense a reduction in the red (660 nm) to far-red (730 nm) light ratio (R/FR) in addition to a general reduction in light intensity. These light signals trigger a spectrum of morphological changes manifested by growth of stem-like tissue (hypocotyl, petiole, etc.) instead of harvestable organs (leaves, fruits, seeds, etc.)-namely, shade avoidance syndrome (SAS). Common phenotypical changes related to SAS are changes in leaf hyponasty, an increase in hypocotyl and internode elongation and extended petioles. Prolonged shade exposure leads to early flowering, less branching, increased susceptibility to insect herbivory, and decreased seed yield. Thus, shade avoidance significantly impacts on agronomic traits. Many genetic and molecular studies have revealed that phytochromes, cryptochromes and UVR8 (UV-B photoreceptor protein) monitor the changes in light intensity under shade and regulate the stability or activity of phytochrome-interacting factors (PIFs). PIF-governed modulation of the expression of auxin biosynthesis, transporter and signaling genes is the major driver for shade-induced hypocotyl elongation. Besides auxin, gibberellins, brassinosteroids, and ethylene are also required for shade-induced hypocotyl or petiole elongation growth. In leaves, accumulated auxin stimulates cytokinin oxidase expression to break down cytokinins and inhibit leaf growth. In the young buds, shade light promotes the accumulation of abscisic acid to repress branching. Shade light also represses jasmonate- and salicylic acid-induced defense responses to balance resource allocation between growth and defense. Here we will summarize recent findings relating to such hormonal regulation in SAS in Arabidopsis thaliana, Brassica rapa, and certain crops.

Trading direct for indirect defense? Phytochrome B inactivation in tomato attenuates direct anti-herbivore defenses whilst enhancing volatile-mediated attraction of predators

Under conditions of competition for light, which lead to the inactivation of the photoreceptor phytochrome B (phyB), the growth of shade-intolerant plants is promoted and the accumulation of direct anti-herbivore defenses is down-regulated. Little is known about the effects of phyB on emissions of volatile organic compounds (VOCs), which play a major role as informational cues in indirect defense. We investigated the effects of phyB on direct and indirect defenses in tomato (Solanum lycopersicum) using two complementary approaches to inactivate phyB: illumination with a low red to far-red ratio, simulating competition, and mutation of the two PHYB genes present in the tomato genome. Inactivation of phyB resulted in low levels of constitutive defenses and down-regulation of direct defenses induced by methyl jasmonate (MeJA). Interestingly, phyB inactivation also had large effects on the blends of VOCs induced by MeJA. Moreover, in two-choice bioassays using MeJA-induced plants, the predatory mirid bug Macrolophus pygmaeus preferred VOCs from plants in which phyB was inactivated over VOCs from control plants. These results suggest that, in addition to repressing direct defense, phyB inactivation has consequences for VOC-mediated tritrophic interactions in canopies, presumably attracting predators to less defended plants, where they are likely to find more abundant prey.

Ethylene- and Shade-Induced Hypocotyl Elongation Share Transcriptome Patterns and Functional Regulators

Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests a possible convergence of the signaling pathways. Shoot elongation is mediated by passive ethylene accumulating to high concentrations in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here, we study hypocotyl elongation as a proxy for shoot elongation and delineate Arabidopsis (Arabidopsis thaliana) hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene- and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared with the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid, and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilize a conserved set of transcriptionally regulated genes to modulate and fine-tune growth.

Involvement of ethylene in gibberellic acid-induced sulfur assimilation, photosynthetic responses, and alleviation of cadmium stress in mustard

The role of gibberellic acid (GA) or sulfur (S) in stimulation of photosynthesis is known. However, information on the involvement of ethylene in GA-induced photosynthetic responses and cadmium (Cd) tolerance is lacking. This work shows that ethylene is involved in S-assimilation, photosynthetic responses and alleviation of Cd stress by GA in mustard (Brassica juncea L.). Plants grown with 200 mg Cd kg(-1) soil were less responsive to ethylene despite high ethylene evolution and showed photosynthetic inhibition. Plants receiving 10 μM GA spraying plus 100 mg S kg(-1) soil supplementation exhibited increased S-assimilation and photosynthetic responses under Cd stress. Application of GA plus S decreased oxidative stress of plants grown with Cd and limited stress ethylene formation to the range suitable for promoting sulfur use efficiency (SUE), glutathione (GSH) production and photosynthesis. The role of ethylene in GA-induced S-assimilation and reversal of photosynthetic inhibition by Cd was substantiated by inhibiting ethylene biosynthesis with the use of aminoethoxyvinylglycine (AVG). The suppression of S-assimilation and photosynthetic responses by inhibiting ethylene in GA plus S treated plants under Cd stress indicated the involvement of ethylene in GA-induced S-assimilation and Cd stress alleviation. The outcome of the study is important to unravel the interaction between GA and ethylene and their role in Cd tolerance in plants.

Molecular control of crop shade avoidance

The shade avoidance response (SAR) in crops can be detrimental to yield, as precious carbon resources are redirected to stem or petiole elongation at the expense of biomass production. While breeding efforts have inadvertently attenuated this response in staple crops through correlated selection for yield at high density, it has not been eliminated. The extensive work done in Arabidopsis has provided a detailed understanding of the SAR and can be used as a framework for understanding the SAR in crop species. Recent crop SAR works point to auxin as a key factor in regulating the SAR in several crop species. These works also clearly demonstrate that one model for crop SAR will not fit all, and thus we need to move forward with studying the genetic players of the SAR in several model crop species. In this review, we provide the current knowledge of the SAR as reported at the physiological and molecular levels.

Plant Responses to Vegetation Proximity: A Whole Life Avoiding Shade

In high density of vegetation, plants detect neighbors by perceiving changes in light quality through phytochrome photoreceptors. Close vegetation proximity might result in competition for resources, such as light. To face this challenge, plants have evolved two alternative strategies: to either tolerate or avoid shade. Shade-avoiding species generally adapt their development by inducing hypocotyl, stem, and petiole elongation, apical dominance and flowering, and decreasing leaf expansion and yield, a set of responses collectively known as the shade avoidance syndrome (SAS). The SAS responses have been mostly studied at the seedling stage, centered on the increase of hypocotyl elongation. After compiling the main findings about SAS responses in seedlings, this review is focused on the response to shade at adult stages of development, such as petioles of adult leaves, and the little information available on the SAS responses in reproductive tissues. We discuss these responses based on the knowledge about the molecular mechanisms and components with a role in regulating the SAS response of the hypocotyls of Arabidopsis thaliana. The transcriptional networks involved in this process, as well as the communication among the tissues that perceive the shade and the ones that respond to this stimulus will also be briefly commented.

Ethylene Signaling Influences Light-Regulated Development in Pea

Plant responses to light involve a complex network of interactions among multiple plant hormones. In a screen for mutants showing altered photomorphogenesis under red light, we identified a mutant with dramatically enhanced leaf expansion and delayed petal senescence. We show that this mutant exhibits reduced sensitivity to ethylene and carries a nonsense mutation in the single pea (Pisum sativum) ortholog of the ethylene signaling gene ETHYLENE INSENSITIVE2 (EIN2). Consistent with this observation, the ein2 mutation rescues the previously described effects of ethylene overproduction in mature phytochrome-deficient plants. In seedlings, ein2 confers a marked increase in leaf expansion under monochromatic red, far-red, or blue light, and interaction with phytochromeA, phytochromeB, and long1 mutants confirms that ein2 enhances both phytochrome- and cryptochrome-dependent responses in a LONG1-dependent manner. In contrast, minimal effects of ein2 on seedling development in darkness or high-irradiance white light show that ethylene is not limiting for development under these conditions. These results indicate that ethylene signaling constrains leaf expansion during deetiolation in pea and provide further evidence that down-regulation of ethylene production may be an important component mechanism in the broader control of photomorphogenic development by phytochrome and cryptochrome.

Illuminating light, cytokinin, and ethylene signalling crosstalk in plant development

Integrating important environmental signals with intrinsic developmental programmes is a crucial adaptive requirement for plant growth, survival, and reproduction. Key environmental cues include changes in several light variables, while important intrinsic (and highly interactive) regulators of many developmental processes include the phytohormones cytokinins (CKs) and ethylene. Here, we discuss the latest discoveries regarding the molecular mechanisms mediating CK/ethylene crosstalk at diverse levels of biosynthetic and metabolic pathways and their complex interactions with light. Furthermore, we summarize evidence indicating that multiple hormonal and light signals are integrated in the multistep phosphorelay (MSP) pathway, a backbone signalling pathway in plants. Inter alia, there are strong overlaps in subcellular localizations and functional similarities in components of these pathways, including receptors and various downstream agents. We highlight recent research demonstrating the importance of CK/ethylene/light crosstalk in selected aspects of plant development, particularly seed germination and early seedling development. The findings clearly demonstrate the crucial integration of plant responses to phytohormones and adaptive responses to environmental cues. Finally, we tentatively identify key future challenges to refine our understanding of the molecular mechanisms mediating crosstalk between light and hormonal signals, and their integration during plant life cycles.

Waterlogging and submergence stress: affects and acclimation

Submergence, whether partial or complete, imparts some serious consequences on plants grown in flood prone ecosystems. Some plants can endure these conditions by embracing various survival strategies, including morphological adaptations and physiological adjustments. This review summarizes recent progress made in understanding of the stress and the acclimation responses of plants under waterlogged or submerged conditions. Waterlogging and submergence are often associated with hypoxia development, which may trigger various morphological traits and cellular acclimation responses. Ethylene, abscisic acid, gibberellic acid and other hormones play a crucial role in the survival process which is controlled genetically. Effects at the cellular level, including ATP management, starch metabolism, elemental toxicity, role of transporters and redox status have been explained. Transcriptional and hormonal interplay during this stress may provide some key aspects in understanding waterlogging and submergence tolerance. The level and degree of tolerance may vary depending on species or climatic variations which need to be studied for a proper understanding of waterlogging stress at the global level. The exploration of regulatory pathways and interplay in model organisms such as Arabidopsis and rice would provide valuable resources for improvement of economically and agriculturally important plants in waterlogging affected areas.

RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean

Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. RNASeq data were collected from six biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed-free controls varied between years to mitigate treatment effects, and to allow detection of general soybean weed responses. Soybean plants were not visibly nutrient- or water-stressed. We identified 55 consistently downregulated genes in weedy plots. Many of the downregulated genes were heat shock genes. Fourteen genes were consistently upregulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the upregulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in Arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest that the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean.

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.

Involvement of cotton gene GhFPF1 in the regulation of shade avoidance responses in Arabidopsis thaliana

Phytochrome system perceives the reduction in the ratio of red to far-red light when plants are grown under dense canopy. This signal, regarded as a warning of competition, will trigger a series of phenotypic changes to avoid shade. Progress has been made for several phytochrome signaling intermediates acting as positive regulators of accelerated elongation growth and promotion of flowering in shade-avoidance has been identified. Recently, a FPF1 homolog GhFPF1 was identified in upland cotton. Our data supported that transgenic Arabidopsis of over-expressing GhFPF1 displayed a constitutive shade-avoiding phenotype resembling phyB mutants in several respects such as accelerated elongation of hypocotyl and petioles, upward of leaf movement, and promoted flowering. In this addendum, by dissection of GhFPF1 acting as a component of shade-avoidance responses we suppose that GhFPF1 might influence the timing of the floral transition independently of shade-mediated early flowering. Furthermore, the opposite changes of IAA content in transgenic leaves and stems suggested that alteration of IAA storage and release took place during shade-avoidance responses.