Plant Strategies for Enhancing Access to Sunlight

Harnessing microbes as sun cream against high light stress

Plants rely on solar energy for growth through photosynthesis, yet excessive light intensity can induce physiological damage. Despite the considerable harm, inadequate attention has been directed toward understanding how plant-associated microorganisms mitigate this stress, and the impact of high light intensity on plant microbial communities remains underexplored. Through this Viewpoint, we aim to highlight the potential of microbial communities to enhance plant resilience and understand how light stress can shape plant microbiome. A full understanding of these dynamics is essential to design strategies that take advantage of microbial assistance to plants under light stress and to effectively manage the impact of changing light conditions on plant-microbe interactions.

ASYMMETRIC LEAVES1 promotes leaf hyponasty in Arabidopsis by light-mediated auxin signaling

In plants, balancing growth and environmental responses is crucial for maximizing fitness. Close proximity among plants and canopy shade, which negatively impacts reproduction, elicits morphological adjustments such as hypocotyl growth and leaf hyponasty, mainly through changes in light quality and auxin levels. However, how auxin, synthesized from a shaded leaf blade, distally induces elongation of hypocotyl and petiole cells remains to be elucidated. We demonstrated that ASYMMETRIC LEAVES1 (AS1) promotes leaf hyponasty through the regulation of auxin biosynthesis, polar auxin transport, and auxin signaling genes in Arabidopsis (Arabidopsis thaliana). AS1 overexpression leads to elongation of the abaxial petiole cells with auxin accumulation in the petiole, resulting in hyponastic growth, which is abolished by the application of an auxin transport inhibitor to the leaf blade. In addition, the as1 mutant exhibits reduced hypocotyl growth under shade conditions. We observed that AS1 protein accumulates in the nucleus in response to shade or far-red light. Chromatin immunoprecipitation analysis identified the association of AS1 with the promoters of YUCCA8 (YUC8) and INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19). In addition, AS1 forms complexes with PHYTOCHROME-INTERACTING FACTORs in the nucleus and synergistically induces YUC8 and IAA19 expression. Our findings suggest that AS1 plays a crucial role in facilitating phenotypic plasticity to the surroundings by connecting light and phytohormone action.

Sextuple knockouts of a highly conserved and coexpressed AUXIN/INDOLE-3-ACETIC ACID gene set confer shade avoidance-like responses in Arabidopsis

AUXIN/INDOLE-3-ACETIC ACIDs are transcriptional repressors for auxin signalling. Aux/IAAs of Arabidopsis thaliana display some functional redundancy. The IAA3/SHY2 clade (IAA1, IAA2, IAA3 and IAA4) show strong sequence similarity, but no higher-order mutants have been reported. Here, through CRISPR/Cas9 genome editing, we generated loss-of-function iaa1/2/3/4 mutants. The quadruple mutants only exhibited a weak phenotype. Thus, we additionally knocked out IAA7/AXR2 and IAA16, which are coexpressed with IAA1/2/3/4. Remarkably, under white light control conditions, the iaa1/2/3/4/7/16 mutants exhibited a shade avoidance-like phenotype with over-elongated hypocotyls and petioles and hyponastic leaves. The sextuple mutants were highly sensitive to low light intensity, and the hypocotyl cells of the mutants were excessively elongated. Transcriptome profiling and qRT-PCR analyses revealed that the sextuple mutation upregulated IAA19/MSG2 and IAA29, two shared shade/auxin signalling targets. Besides, genes encoding cell wall-remodelling proteins and shade-responsive transcription regulators were upregulated. Using dual-luciferase reporter assays, we verified that IAA2/IAA7 targeted the promoters of cell wall-remodelling genes to inhibit their transcription. Our work indicates that the IAA1/2/3/4/7/16 gene set is required for the optimal integration of auxin and shade signalling. The mutants generated here should be valuable for exploring the complex interactions among signal sensors, transcription activators and transcription repressors during hormone/environmental responses.

Temporal and spatial frameworks supporting plant responses to vegetation proximity

After the perception of vegetation proximity by phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the shade avoidance syndrome (SAS). Shade perception by the phytochrome B (phyB) photoreceptor unleashes the PHYTOCHROME INTERACTING FACTORs and initiates SAS responses. In Arabidopsis (Arabidopsis thaliana) seedlings, shade perception involves rapid and massive changes in gene expression, increases auxin production, and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5, also participate in the shade regulation of the hypocotyl elongation response by repressing it. However, why and how so many regulators with either positive or negative activities modulate the same response remains unclear. Our physiological, genetic, cellular, and transcriptomic analyses showed that (i) these components are organized into 2 main branches or modules and (ii) the connection between them is dynamic and changes with the time of shade exposure. We propose a model for the regulation of shade-induced hypocotyl elongation in which the temporal and spatial functional importance of the various SAS regulators analyzed here helps to explain the coexistence of differentiated regulatory branches with overlapping activities.

Comparative Insights into Photosynthetic, Biochemical, and Ultrastructural Mechanisms in Hibiscus and Pelargonium Plants

Understanding photosynthetic mechanisms in different plant species is crucial for advancing agricultural productivity and ecological restoration. This study presents a detailed physiological and ultrastructural comparison of photosynthetic mechanisms between Hibiscus (Hibiscus rosa-sinensis L.) and Pelargonium (Pelargonium zonale (L.) L'Hér. Ex Aiton) plants. The data collection encompassed daily photosynthetic profiles, responses to light and CO2, leaf optical properties, fluorescence data (OJIP transients), biochemical analyses, and anatomical observations. The findings reveal distinct morphological, optical, and biochemical adaptations between the two species. These adaptations were associated with differences in photochemical (AMAX, E, Ci, iWUE, and α) and carboxylative parameters (VCMAX, ΓCO2, gs, gm, Cc, and AJMAX), along with variations in fluorescence and concentrations of chlorophylls and carotenoids. Such factors modulate the efficiency of photosynthesis. Energy dissipation mechanisms, including thermal and fluorescence pathways (ΦPSII, ETR, NPQ), and JIP test-derived metrics highlighted differences in electron transport, particularly between PSII and PSI. At the ultrastructural level, Hibiscus exhibited optimised cellular and chloroplast architecture, characterised by increased chloroplast density and robust grana structures. In contrast, Pelargonium displayed suboptimal photosynthetic parameters, possibly due to reduced thylakoid counts and a higher proportion of mitochondria. In conclusion, while Hibiscus appears primed for efficient photosynthesis and energy storage, Pelargonium may prioritise alternative cellular functions, engaging in a metabolic trade-off.

Far-red light increases maize volatile emissions in response to volatile cues from neighbouring plants

Plants perceive the presence and defence status of their neighbours through light and volatile cues, but how plants integrate both stimuli is poorly understood. We investigated if and how low Red to Far red light (R:FR) ratios, indicative of shading or canopy closure, affect maize (Zea mays) responses to herbivore-induced plant volatiles (HIPVs), including the green leaf volatile (Z)-3-hexenyl acetate. We modulated light signalling and perception by using FR supplementation and a phyB1phyB2 mutant, and we determined volatile release as a response readout. To gain mechanistic insights, we examined expression of volatile biosynthesis genes, hormone accumulation, and photosynthesis. Exposure to a full blend of HIPVs or (Z)-3-hexenyl acetate induced maize volatile release. Short-term FR supplementation increased this response. In contrast, prolonged FR supplementation or constitutive phytochrome B inactivation in phyB1phyB2 plants showed the opposite response. Short-term FR supplementation enhanced photosynthesis and stomatal conductance and (Z)-3-hexenyl acetate-induced JA-Ile levels. We conclude that a FR-enriched light environment can prompt maize plants to respond more strongly to HIPVs emitted by neighbours, which might be explained by changes in photosynthetic processes and phytochrome B signalling. Our findings reveal interactive responses to light and volatile cues with potentially important consequences for plant-plant and plant-herbivore interactions.

Variation in Leaf Functional Traits of Populus laurifolia Ldb and Ulmus pumila L. Across Five Contrasting Urban Sites in Ulaanbaatar, Mongolia

Amid urbanization, studying leaf functional traits of woody plants in urban environments is essential for understanding how urban green spaces function and how they can be effectively managed sustainably. In this study, we investigated the effects of different growing conditions on the morpho-physiological traits of Populus laurifolia and Ulmus pumila across five contrasting urban sites. The leaf area (LA), leaf length (LL), leaf width (LW), leaf biomass (LB), specific leaf area (SLA), leaf chlorophyll concentration, chlorophyll fluorescence parameters, leaf water potential at predawn (Ψpd) and midday (Ψmd), leaf performance index (PIabs), and phenotypic plasticity index (PPI) were compared across five contrasting urban sites. The soil chemical and physical properties were also compared between sites. There were significant differences in soil physicochemical characteristics between sites. We found significant effects of site on most of the morpho-physiological traits measured, except for Ψmd. The leaf chlorophyll concentration of P. laurifolia and U. pumila varied significantly between sites. The Ψpd was significantly different between years and sites. In U. pumila, the mean PPI for morphological traits (0.20) was lower than that for physiological traits (0.21). In conclusion, we revealed significant variations in the morpho-physiological traits of P. laurifolia and U. pumila across the five urban sites. Hence, long-term, large-scale studies are recommended to examine how diverse species respond to different urban growing conditions and to include other ecologically important plant traits for a better understanding of urban trees in a changing environment.

Comparative Analysis of Volatile Compounds and Biochemical Activity of Curcuma xanthorrhiza Roxb. Essential Oil Extracted from Distinct Shaded Plants

The application of shade during plants' growth significantly alters the biochemical compounds of the essential oil (EO). We aimed to analyze the effect of shade on the volatile compounds and biochemical activities of EO extracted from Curcuma xanthorrhiza Roxb. (C. xanthorrhiza) plants. Four shading conditions were applied: no shading (S0), 25% (S25), 50% (S50), and 75% shade (S75). The volatile compounds of EO extracted from each shaded plant were analyzed by gas chromatography-mass spectrometry. The antioxidant, antibacterial, and antiproliferative activities of EO were also investigated. We found that shade application significantly reduced the C. xanthorrhiza EO yield but increased its aroma and bioactive compound concentration. α-curcumene, xanthorrhizol, α-cedrene, epicurzerenone, and germacrone were found in EO extracted from all conditions. However, β-bisabolol, curzerene, curcuphenol, and γ-himachalene were only detected in the EO of S75 plants. The EO of the shaded plants also showed higher antioxidant activity as compared to unshaded ones. In addition, the EO extracted from S75 exerted higher antiproliferative activity on HeLa cells as compared to S0. The EO extracted from S0 and S25 showed higher antibacterial activity against Gram-positive bacteria than kanamycin. Our results suggest that shade applications alter the composition of the extractable volatile compounds in C. xanthorrhiza, which may result in beneficial changes in the biochemical activity of the EO.

Far-red light enrichment affects gene expression and architecture as well as growth and photosynthesis in rice

Plants use light as a resource and signal. Photons within the 400-700 nm waveband are considered photosynthetically active. Far-red photons (FR, 700-800 nm) are used by plants to detect nearby vegetation and elicit the shade avoidance syndrome. In addition, FR photons have also been shown to contribute to photosynthesis, but knowledge about these dual effects remains scarce. Here, we study shoot-architectural and photosynthetic responses to supplemental FR light during the photoperiod in several rice varieties. We observed that FR enrichment only mildly affected the rice transcriptome and shoot architecture as compared to established model species, whereas leaf formation, tillering and biomass accumulation were clearly promoted. Consistent with this growth promotion, we found that CO2-fixation in supplemental FR was strongly enhanced, especially in plants acclimated to FR-enriched conditions as compared to control conditions. This growth promotion dominates the effects of FR photons on shoot development and architecture. When substituting FR enrichment with an end-of-day FR pulse, this prevented photosynthesis-promoting effects and elicited shade avoidance responses. We conclude that FR photons can have a dual role, where effects depend on the environmental context: in addition to being an environmental signal, they are also a potent source of harvestable energy.

Maize smart-canopy architecture enhances yield at high densities

Increasing planting density is a key strategy for enhancing maize yields1-3. An ideotype for dense planting requires a 'smart canopy' with leaf angles at different canopy layers differentially optimized to maximize light interception and photosynthesis4-6, among other features. Here we identified leaf angle architecture of smart canopy 1 (lac1), a natural mutant with upright upper leaves, less erect middle leaves and relatively flat lower leaves. lac1 has improved photosynthetic capacity and attenuated responses to shade under dense planting. lac1 encodes a brassinosteroid C-22 hydroxylase that predominantly regulates upper leaf angle. Phytochrome A photoreceptors accumulate in shade and interact with the transcription factor RAVL1 to promote its degradation via the 26S proteasome, thereby inhibiting activation of lac1 by RAVL1 and decreasing brassinosteroid levels. This ultimately decreases upper leaf angle in dense fields. Large-scale field trials demonstrate that lac1 boosts maize yields under high planting densities. To quickly introduce lac1 into breeding germplasm, we transformed a haploid inducer and recovered homozygous lac1 edits from 20 diverse inbred lines. The tested doubled haploids uniformly acquired smart-canopy-like plant architecture. We provide an important target and an accelerated strategy for developing high-density-tolerant cultivars, with lac1 serving as a genetic chassis for further engineering of a smart canopy in maize.

GIGANTEA adjusts the response to shade at dusk by directly impinging on PHYTOCHROME INTERACTING FACTOR 7 function

For plants adapted to bright light, a decrease in the amount of light received can be detrimental to their growth and survival. Consequently, in response to shade from surrounding vegetation, they initiate a suite of molecular and morphological changes known as the shade avoidance response through which stems and petioles elongate in search for light. Under sunlight-night cycles, the plant's responsiveness to shade varies across the day, being maximal at dusk time. While a role for the circadian clock in this regulation has long been proposed, mechanistic understanding of how it is achieved is incomplete. Here, we show that the clock component GIGANTEA (GI) directly interacts with the transcriptional regulator PHYTOCHROME INTERACTING FACTOR 7 (PIF7), a key player in the response to shade. GI represses PIF7 transcriptional activity and the expression of its target genes in response to shade, thereby fine-tuning the magnitude of the response to limiting light conditions. We find that under light/dark cycles, this function of GI is required to adequately modulate the gating of the response to shade at dusk. Importantly, we also show that this circuit primarily operates in epidermal cells, highlighting the relevance of tissue-specific clock-output connections for the regulation of plant development in resonance with the environment.

Environmental Control of Hypocotyl Elongation

The hypocotyl is the embryonic stem connecting the primary root to the cotyledons. Hypocotyl length varies tremendously depending on the conditions. This developmental plasticity and the simplicity of the organ explain its success as a model for growth regulation. Light and temperature are prominent growth-controlling cues, using shared signaling elements. Mechanisms controlling hypocotyl elongation in etiolated seedlings reaching the light differ from those in photoautotrophic seedlings. However, many common growth regulators intervene in both situations. Multiple photoreceptors including phytochromes, which also respond to temperature, control the activity of several transcription factors, thereby eliciting rapid transcriptional reprogramming. Hypocotyl growth often depends on sensing in green tissues and interorgan communication comprising auxin. Hypocotyl auxin, in conjunction with other hormones, determines epidermal cell elongation. Plants facing cues with opposite effects on growth control hypocotyl elongation through intricate mechanisms. We discuss the status of the field and end by highlighting open questions.

What is going on inside of phytochrome B photobodies?

Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.

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.

The asymmetric expression of plasma membrane H+-ATPase family genes in response to pulvinus-driven leaf phototropism movement in Vitis vinifera

Phototropism movement is crucial for plants to adapt to various environmental changes. Plant P-type H+-ATPase (HA) plays diverse roles in signal transduction during cell expansion, regulation of cellular osmotic potential and stomatal opening, and circadian movement. Despite numerous studies on the genome-wide analysis of Vitis vinifera, no research has been done on the P-type H+-ATPase family genes, especially concerning pulvinus-driven leaf movement. In this study, 55 VvHAs were identified and classified into nine distinct subgroups (1 to 9). Gene members within the same subgroups exhibit similar features in motif, intron/exon, and protein tertiary structures. Furthermore, four pairs of genes were derived by segmental duplication in grapes. Cis-acting element analysis identified numerous light/circadian-related elements in the promoters of VvHAs. qRT-PCR analysis showed that several genes of subgroup 7 were highly expressed in leaves and pulvinus during leaf movement, especially VvHA14, VvHA15, VvHA16, VvHA19, VvHA51, VvHA52, and VvHA54. Additionally, we also found that the VvHAs genes were asymmetrically expressed on both sides of the extensor and flexor cell of the motor organ, the pulvinus. The expression of VvHAs family genes in extensor cells was significantly higher than that in flexor cells. Overall, this study serves as a foundation for further investigations into the functions of VvHAs and contributes to the complex mechanisms underlying grapevine pulvinus growth and development.

Mechanism of the Pulvinus-Driven Leaf Movement: An Overview

Leaf movement is a manifestation of plant response to the changing internal and external environment, aiming to optimize plant growth and development. Leaf movement is usually driven by a specialized motor organ, the pulvinus, and this movement is associated with different changes in volume and expansion on the two sides of the pulvinus. Blue light, auxin, GA, H+-ATPase, K+, Cl-, Ca2+, actin, and aquaporin collectively influence the changes in water flux in the tissue of the extensor and flexor of the pulvinus to establish a turgor pressure difference, thereby controlling leaf movement. However, how these factors regulate the multicellular motility of the pulvinus tissues in a species remains obscure. In addition, model plants such as Medicago truncatula, Mimosa pudica, and Samanea saman have been used to study pulvinus-driven leaf movement, showing a similarity in their pulvinus movement mechanisms. In this review, we summarize past research findings from the three model plants, and using Medicago truncatula as an example, suggest that genes regulating pulvinus movement are also involved in regulating plant growth and development. We also propose a model in which the variation of ion flux and water flux are critical steps to pulvinus movement and highlight questions for future research.

Pectin methylesterification state and cell wall mechanical properties contribute to neighbor proximity-induced hypocotyl growth in Arabidopsis

Plants growing with neighbors compete for light and consequently increase the growth of their vegetative organs to enhance access to sunlight. This response, called shade avoidance syndrome (SAS), involves photoreceptors such as phytochromes as well as phytochrome interacting factors (PIFs), which regulate the expression of growth-mediating genes. Numerous cell wall-related genes belong to the putative targets of PIFs, and the importance of cell wall modifications for enabling growth was extensively shown in developmental models such as dark-grown hypocotyl. However, the contribution of the cell wall in the growth of de-etiolated seedlings regulated by shade cues remains poorly established. Through analyses of mechanical and biochemical properties of the cell wall coupled with transcriptomic analysis of cell wall-related genes from previously published data, we provide evidence suggesting that cell wall modifications are important for neighbor proximity-induced elongation. Further analysis using loss-of-function mutants impaired in the synthesis and remodeling of the main cell wall polymers corroborated this. We focused on the cgr2cgr3 double mutant that is defective in methylesterification of homogalacturonan (HG)-type pectins. By following hypocotyl growth kinetically and spatially and analyzing the mechanical and biochemical properties of cell walls, we found that methylesterification of HG-type pectins was required to enable global cell wall modifications underlying neighbor proximity-induced hypocotyl growth. Collectively, our work suggests that plant competition for light induces changes in the expression of numerous cell wall genes to enable modifications in biochemical and mechanical properties of cell walls that contribute to neighbor proximity-induced growth.

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.

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controls shade avoidance syndrome in Arabidopsis

The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loops) and modulating local three-dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far-red (FR) light, expression of APOLO anti-correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far-red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far-red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant-environment interactions may therefore become a new tool for sustainable agriculture.

HISTONE DEACETYLASE 9 promotes hypocotyl-specific auxin response under shade

Vegetative shade causes an array of morphological changes in plants called shade avoidance syndrome, which includes hypocotyl and petiole elongation, leaf hyponasty, reduced leaf growth, early flowering and rapid senescence. Here, we show that loss-of-function mutations in HISTONE DEACETYLASE 9 (HDA9) attenuated the shade-induced hypocotyl elongation in Arabidopsis. However, the hda9 cotyledons and petioles under shade were not significantly different from those in wild-type, suggesting a specific function of HDA9 in hypocotyl elongation in response to shade. HDA9 expression levels were stable under shade and its protein was ubiquitously detected in cotyledon, hypocotyl and root. Organ-specific transcriptome analysis unraveled that shade induced a set of auxin-responsive genes, such as SMALL AUXIN UPREGULATED RNAs (SAURs) and AUXIN/INDOLE-3-ACETIC ACIDs (AUX/IAAs) and their induction was impaired in hda9-1 hypocotyls. In addition, HDA9 binding to loci of SAUR15/65, IAA5/6/19 and ACS4 was increased under shade. The genetic and organ-specific gene expression analyses further revealed that HDA9 may cooperate with PHYTOCHROME-INTERACTING FACTOR 4/7 in the regulation of shade-induced hypocotyl elongation. Furthermore, HDA9 and PIF7 proteins were found to interact together and thus it is suggested that PIF7 may recruit HDA9 to regulate the shade/auxin responsive genes in response to shade. Overall, our study unravels that HDA9 can work as one component of a hypocotyl-specific transcriptional regulatory machinery that activates the auxin response at the hypocotyl leading to the elongation of this organ under shade.

Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics

Plants detect their neighbors via various cues, including reflected light and touching of leaf tips, which elicit upward leaf movement (hyponasty). It is currently unknown how touch is sensed and how the signal is transferred from the leaf tip to the petiole base that drives hyponasty. Here, we show that touch-induced hyponasty involves a signal transduction pathway that is distinct from light-mediated hyponasty. We found that mechanostimulation of the leaf tip upon touching causes cytosolic calcium ([Ca2+]cyt induction in leaf tip trichomes that spreads towards the petiole. Both perturbation of the calcium response and the absence of trichomes reduce touch-induced hyponasty. Finally, using plant competition assays, we show that touch-induced hyponasty is adaptive in dense stands of Arabidopsis. We thus establish a novel, adaptive mechanism regulating hyponastic leaf movement in response to mechanostimulation by neighbors in dense vegetation.

Foliar application of silicon sources and shading levels in Peltophorum dubium (Spreng.) Taub

Depending on the intensity and ecological successional classification of plants, light availability can become an unfavorable condition for producing high-quality seedlings. We hypothesized that applying silicon sources might contribute to inducing tolerance to different shading levels for Peltophorum dubium (Spreng.) Taub. seedlings. Two independent experiments were developed: I) the application of five doses of silicon oxide (SiO2: 0.0; 1.0; 2.0; 4.0; and 6.0 g L-1); and II) the application of five doses of potassium silicate (K2SiO3: 0.0; 5.0; 10.0; 15.0; and 20.0 mL L-1 of water). Both were associated with three shading levels: 0% (direct sunlight), 30%, and 50%. In experiment I, we observed that seedlings were more responsive to shading levels and had little influence from foliar application of SiO2, with higher growth, biomass, and quality values when grown under direct sunlight (0% shading). In experiment II, the foliar application of 20.0 mL L-1 of K2SiO3 contributed to greater heights under 0% and 30% shading. Meanwhile, under 50% shading, the dose of 5.0 K2SiO3 favored the species' growth. The application of K2SiO3 favored the increase in the dry mass of the aerial part (DMAP). The highest biomass production and seedling quality occurred under 0% and 30% shading. The 50% shaded environment was most unfavorable to the growth and quality of P. dubium seedlings. Even though the seedlings were not very responsive to silicon sources, K2SiO3 provided a greater response than SiO2. High-quality seedling production is favored when the seedlings are grown under direct sunlight (0% shading).

ELONGATED HYPOCOTYL5 (HY5) and HY5 HOMOLOGUE (HYH) maintain shade avoidance suppression in UV-B

Reductions in red to far-red ratio (R:FR) provide plants with an unambiguous signal of vegetational shade and are monitored by phytochrome photoreceptors. Plants integrate this information with other environmental cues to determine the proximity and density of encroaching vegetation. Shade-sensitive species respond to reductions in R:FR by initiating a suite of developmental adaptations termed shade avoidance. These include the elongation of stems to facilitate light foraging. Hypocotyl elongation is driven by increased auxin biosynthesis promoted by PHYTOCHROME INTERACTING FACTORs (PIF) 4, 5 and 7. UV-B perceived by the UV RESISTANCE LOCUS 8 (UVR8) photoreceptor rapidly inhibits shade avoidance, in part by suppressing PIF4/5 transcript accumulation and destabilising PIF4/5 protein. Here, we show that longer-term inhibition of shade avoidance is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOGUE (HYH), which regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification. HY5 and HYH are elevated in UV-B and suppress the expression of XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) genes involved in cell wall loosening. They additionally increase expression GA2-OXIDASE1 (GA2ox1) and GA2ox2, encoding gibberellin catabolism enzymes that act redundantly to stabilise the PIF-inhibiting DELLA proteins. UVR8 therefore regulates temporally distinct signalling pathways to first rapidly inhibit and subsequently maintain suppression of shade avoidance following UV-B exposure.

The Importance of Using Realistic 3D Canopy Models to Calculate Light Interception in the Field

Quantifying canopy light interception provides insight into the effects of plant spacing, canopy structure, and leaf orientation on radiation distribution. This is essential for increasing crop yield and improving product quality. Canopy light interception can be quantified using 3-dimensional (3D) plant models and optical simulations. However, virtual 3D canopy models (VCMs) have often been used to quantify canopy light interception because realistic 3D canopy models (RCMs) are difficult to obtain in the field. This study aims to compare the differences in light interception between VCMs and RCM. A realistic 3D maize canopy model (RCM) was reconstructed over a large area of the field using an advanced unmanned aerial vehicle cross-circling oblique (CCO) route and the structure from motion-multi-view stereo method. Three types of VCMs (VCM-1, VCM-4, and VCM-8) were then created by replicating 1, 4, and 8 individual realistic plants constructed by CCO in the center of the corresponding RCM. The daily light interception per unit area (DLI), as computed for the 3 VCMs, exhibited marked deviation from the RCM, as evinced by the relative root mean square error (rRMSE) values of 20.22%, 17.38%, and 15.48%, respectively. Although this difference decreased as the number of plants used to replicate the virtual canopy increased, rRMSE of DLI for VCM-8 and RCM still reached 15.48%. It was also found that the difference in light interception between RCMs and VCMs was substantially smaller in the early stage (48 days after sowing [DAS]) than in the late stage (70 DAS). This study highlights the importance of using RCM when calculating light interception in the field, especially in the later growth stages of plants.

Phytochrome-interacting factor PIF3 integrates phytochrome B and UV-B signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls

In Arabidopsis, the photoreceptors phytochrome B (PhyB) and UV-B resistance 8 (UVR8) mediate light responses that play a major role in regulating photomorphogenic hypocotyl growth, but how they crosstalk to coordinate this process is not well understood. Here we report map-based cloning and functional characterization of an ultraviolet (UV)-B-insensitive, long-hypocotyl mutant, lh1, and a wild-type-like mutant, lh2, in cucumber (Cucumis sativus), which show defective CsPhyB and GA oxidase2 (CsGA20ox-2), a key gibberellic acid (GA) biosynthesis enzyme, respectively. The lh2 mutation was epistatic to lh1 and partly suppressed the long-hypocotyl phenotype in the lh1lh2 double mutant. We identified phytochrome interacting factor (PIF) CsPIF3 as playing a critical role in integrating the red/far-red and UV-B light responses for hypocotyl growth. We show that two modules, CsPhyB-CsPIF3-CsGA20ox-2-DELLA and CsPIF3-auxin response factor 18 (CsARF18), mediate CsPhyB-regulated hypocotyl elongation through GA and auxin pathways, respectively, in which CsPIF3 binds to the G/E-box motifs in the promoters of CsGA20ox-2 and CsARF18 to regulate their expression. We also identified a new physical interaction between CsPIF3 and CsUVR8 mediating CsPhyB-dependent, UV-B-induced hypocotyl growth inhibition. Our work suggests that hypocotyl growth in cucumber involves a complex interplay of multiple photoreceptor- and phytohormone-mediated signaling pathways that show both conservation with and divergence from those in Arabidopsis.

Age Determination and Growth Characteristics of the Potentilla griffithii: A Comparison of Two Different Habitats in Western Sichuan Plateau, China

This study proposes a rapid and non-destructive technique for determining the age of Potentilla griffithii individuals in the field by observing the sequence of leaf scars. Based on two- to three-year-old P. griffithii seedlings, planted in a common garden in the western Sichuan Plateau, China, the study found that the rates of basal leaf production were consistent, with leaves growing from March to April and falling off from October to December, leaving behind basal leaf scars. Thus, the age of individuals in situ could be determined by counting the leaf scars. Through this method, we determined the age structure and growth strategy of P. griffithii populations in two typical habitats in the western Sichuan Plateau. In open land habitats, the age structure of P. griffithii populations was relatively younger compared to understory habitats. In open land, P. griffithii tends to allocate more photosynthate terminal organs (leaves and fine roots) to absorbing more resources, as well as to its reproductive organs (flower stems and aggregate fruits), to expand the population. The P. griffithii population in the understory habitat is in its middle-age stage and concentrates more photosynthate in the coarse root part (e.g., the high coarse root mass fraction (FRMF)) to support the plant. Additionally, we found a significant correlation between P. griffithii plant age and various traits in open land habitats. Therefore, we conclude that plant age can be used as a good predictor of plant growth condition in open land. These results allow for predicting ecological processes, based on the ages and traits of P. griffithii plants, providing a theoretical basis to support the large-scale breeding of P. griffithii.

SALT OVERLY SENSITIVE2 stabilizes phytochrome-interacting factors PIF4 and PIF5 to promote Arabidopsis shade avoidance

Sun-loving plants trigger the shade avoidance syndrome (SAS) to compete against their neighbors for sunlight. Phytochromes are plant red (R) and far-red (FR) light photoreceptors that play a major role in perceiving the shading signals and triggering SAS. Shade induces a reduction in the level of active phytochrome B (phyB), thus increasing the abundance of PHYTOCHROME-INTERACTING FACTORS (PIFs), a group of growth-promoting transcription factors. However, whether other factors are involved in modulating PIF activity in the shade remains largely obscure. Here, we show that SALT OVERLY SENSITIVE2 (SOS2), a protein kinase essential for salt tolerance, positively regulates SAS in Arabidopsis thaliana. SOS2 directly phosphorylates PIF4 and PIF5 at a serine residue close to their conserved motif for binding to active phyB. This phosphorylation thus decreases their interaction with phyB and posttranslationally promotes PIF4 and PIF5 protein accumulation. Notably, the role of SOS2 in regulating PIF4 and PIF5 protein abundance and SAS is more prominent under salt stress. Moreover, phyA and phyB physically interact with SOS2 and promote SOS2 kinase activity in the light. Collectively, our study uncovers an unexpected role of salt-activated SOS2 in promoting SAS by modulating the phyB-PIF module, providing insight into the coordinated response of plants to salt stress and shade.

Projecting Podocarpaceae response to climate change: we are not out of the woods yet

Under the changing climate, the persistence of Afrotemperate taxa may be threatened as suitable habitat availability decreases. The unique disjunct ranges of podocarps in southern Africa raise questions about the persistence of these species under climate change. Here, we identified likely environmental drivers of these distributions, characterized the current and future (2070) environmental niches, and projected distributions of four podocarp species in South Africa. Species distribution models were conducted using species locality data for Afrocarpus falcatus, Podocarpus latifolius, Pseudotropheus elongatus and Podocarpus henkelii and both historical climate data (1970-2000) and future climate scenarios (Representative Concentration Pathway [RCP] 4.5 and 8.5, 2061-2080) to estimate the current and future distributions. We also used this opportunity to identify the most important climatic variables that likely govern each species' distribution. Using niche overlap estimates, a similarity test, and indices of niche expansion, stability and unfilling, we explored how niches change under different climate scenarios. The distribution of the study species was governed by the maximum temperature of the warmest month, temperature annual range, mean temperature of the wettest quarter, and precipitation of the wettest, driest and warmest quarters. The current distribution of A. falcatus was predicted to expand to higher elevations under RCP 4.5 and RCP 8.5. Podocarpus henkelii was predicted to lose most of its suitable habitat under RCP 4.5 and expand under RCP 8.5; however, this was the opposite for P. elongatus and P. latifolius. Interestingly, P. elongatus, which had the smallest geographic distribution, showed the most vulnerability to climate change in comparison to the other podocarps. Mapping the distribution of podocarps and understanding the differences in their current and future climate niches provide insight into potential climate drivers of podocarp persistence and the potential for adaptation of these species. Overall, these results suggest that P. elongatus and P. henkelii may expand to novel environmental niches.

Photosystems under high light stress: throwing light on mechanism and adaptation

High light stress decreases the photosynthetic rate in plants due to photooxidative damage to photosynthetic apparatus, photoinhibition of PSII, and/or damage to PSI. The dissipation of excess energy by nonphotochemical quenching and degradation of the D1 protein of PSII and its repair cycle help against photooxidative damage. Light stress also activates stress-responsive nuclear genes through the accumulation of phosphonucleotide-3'-phosphoadenosine-5'-phosphate, methylerythritol cyclodiphosphate, and reactive oxygen species which comprise the chloroplast retrograde signaling pathway. Additionally, hormones, such as abscisic acid, cytokinin, brassinosteroids, and gibberellins, play a role in acclimation to light fluctuations. Several alternate electron flow mechanisms, which offset the excess of electrons, include activation of plastid or plastoquinol terminal oxidase, cytochrome b 6/f complex, cyclic electron flow through PSI, Mehler ascorbate peroxidase pathway or water-water cycle, mitochondrial alternative oxidase pathway, and photorespiration. In this review, we provided insights into high light stress-mediated damage to photosynthetic apparatus and strategies to mitigate the damage by decreasing antennae size, enhancing NPQ through the introduction of mutants, expression of algal proteins to improve photosynthetic rates and engineering ATP synthase.

Epidermal GIGANTEA adjusts the response to shade at dusk by directly impinging on PHYTOCHROME INTERACTING FACTOR 7 function

For plants adapted to bright light, a decrease in the amount of light received can be detrimental to their growth and survival. Consequently, in response to shade from surrounding vegetation, they initiate a suite of molecular and morphological changes known as the shade avoidance response (SAR) through which stems and petioles elongate in search for light. Under sunlight-night cycles, the plant's responsiveness to shade varies across the day, being maximal at dusk time. While a role for the circadian clock in this regulation has long been proposed, mechanistic understanding of how it is achieved is incomplete. Here we show that the clock component GIGANTEA (GI) directly interacts with the transcriptional regulator PHYTOCHROME INTERACTING FACTOR 7 (PIF7), a key player in the response to shade. GI represses PIF7 transcriptional activity and the expression of its target genes in response to shade, thereby fine-tuning the magnitude of the response to limiting light conditions. We find that, under light/dark cycles, this function of GI is required to adequately modulate the gating of the response to shade at dusk. Importantly, we also show that GI expression in epidermal cells is sufficient for proper SAR regulation.

Generation of High-Value Genomic Resource in Rice: A “Subgenomic Library” of Low-Light Tolerant Rice Cultivar Swarnaprabha

Rice is the major staple food crop for more than 50% of the world’s total population, and its production is of immense importance for global food security. As a photophilic plant, its yield is governed by the quality and duration of light. Like all photosynthesizing plants, rice perceives the changes in the intensity of environmental light using phytochromes as photoreceptors, and it initiates a morphological response that is termed as the shade-avoidance response (SAR). Phytochromes (PHYs) are the most important photoreceptor family, and they are primarily responsible for the absorption of the red (R) and far-red (FR) spectra of light. In our endeavor, we identified the morphological differences between two contrasting cultivars of rice: IR-64 (low-light susceptible) and Swarnaprabha (low-light tolerant), and we observed the phenological differences in their growth in response to the reduced light conditions. In order to create genomic resources for low-light tolerant rice, we constructed a subgenomic library of Swarnaprabha that expedited our efforts to isolate light-responsive photoreceptors. The titer of the library was found to be 3.22 × 105 cfu/mL, and the constructed library comprised clones of 4–9 kb in length. The library was found to be highly efficient as per the number of recombinant clones. The subgenomic library will serve as a genomic resource for the Gramineae community to isolate photoreceptors and other genes from rice.

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.

Discovering cooperative traits in crop plants

Plants should cooperate, but do they? What does plant cooperation look like? A study in PLOS Biology demonstrates a practical and powerful methodology for exploring plant cooperation.

A combination of plasma membrane sterol biosynthesis and autophagy is required for shade-induced hypocotyl elongation

Plant growth ultimately depends on fixed carbon, thus the available light for photosynthesis. Due to canopy light absorption properties, vegetative shade combines low blue (LB) light and a low red to far-red ratio (LRFR). In shade-avoiding plants, these two conditions independently trigger growth adaptations to enhance light access. However, how these conditions, differing in light quality and quantity, similarly promote hypocotyl growth remains unknown. Using RNA sequencing we show that these two features of shade trigger different transcriptional reprogramming. LB induces starvation responses, suggesting a switch to a catabolic state. Accordingly, LB promotes autophagy. In contrast, LRFR induced anabolism including expression of sterol biosynthesis genes in hypocotyls in a manner dependent on PHYTOCHROME-INTERACTING FACTORs (PIFs). Genetic analyses show that the combination of sterol biosynthesis and autophagy is essential for hypocotyl growth promotion in vegetative shade. We propose that vegetative shade enhances hypocotyl growth by combining autophagy-mediated recycling and promotion of specific lipid biosynthetic processes.

Plants subject to vegetative shade receive a low quantity of blue light (LB) and a low ratio of red to far-red light (LFLR). Here the authors show that while LB induces autophagy, LFLR leads to changes in lipid metabolism, and propose that these processes may contribute to shade avoidance responses.

Phytochrome-Dependent Regulation of ZFP6 and ZFPH Impacts Photomorphogenesis in Arabidopsis thaliana

Phytochromes (phy) are key regulators of photomorphogenesis in plants. Among the different phys characterized in higher plants (i.e., phyA to phyE), phyA and phyB primarily regulate phenotypic responses in plants under far-red (FR) and red (R) conditions, respectively. Recent findings suggest that some zinc finger proteins (ZFPs) are involved in plant light-modulated morphogenesis. However, the interaction(s) between phyA, phyB and ZFP homologs potentially involved in photomorphogenesis, as well as their phenotypic and molecular effects in Arabidopsis seedlings exposed to R and FR light remain to be elucidated fully. Prior analyses with phytochrome chromophore deficient lines indicated that ZFP6 expression is misregulated compared to levels in Col-0 wild type (WT). Here, we used plants with phytochrome chromophore or apoprotein (specifically phyA and phyB) deficiencies, lines with mutations in ZFP6 and ZFP6 HOMOLOG (ZFPH) genes, and plants overexpressing ZFP6 to examine regulatory interactions between phytochromes, ZFP6, and ZFPH. Our results indicate that phytochromes are required for downregulation of ZFP6 and ZFPH and suggest a role for light-regulated control of ZFP levels in phytochrome-dependent photomorphogenesis. Conversely, PHYB is downregulated in zfp6 mutants under R light. Analyses of a zfp6zfph double mutant confirmed disruption in photomorphogenic phenotypes, including the regulation of hypocotyl elongation in seedlings grown under FR light. In addition, PIF3 and PIF4 levels are transcriptionally regulated by ZFP6 and ZFPH in a gibberellic acid-dependent manner. ZFP6 overexpression resulted in opposite phenotypic responses to those observed in the zfp6 and zfph mutants grown in FR and R light, as well as a reduction in the rosette size of mature ZFP6 OX plants relative to WT under white light. Based on these observations, we provide insight into how phy and ZFPs interact to regulate specific aspects of light-dependent processes in Arabidopsis.

Shade suppresses wound-induced leaf repositioning through a mechanism involving PHYTOCHROME KINASE SUBSTRATE (PKS) genes

Shaded plants challenged with herbivores or pathogens prioritize growth over defense. However, most experiments have focused on the effect of shading light cues on defense responses. To investigate the potential interaction between shade-avoidance and wounding-induced Jasmonate (JA)-mediated signaling on leaf growth and movement, we used repetitive mechanical wounding of leaf blades to mimic herbivore attacks. Phenotyping experiments with combined treatments on Arabidopsis thaliana rosettes revealed that shade strongly inhibits the wound effect on leaf elevation. By contrast, petiole length is reduced by wounding both in the sun and in the shade. Thus, the relationship between the shade and wounding/JA pathways varies depending on the physiological response, implying that leaf growth and movement can be uncoupled. Using RNA-sequencing, we identified genes with expression patterns matching the hyponastic response (opposite regulation by both stimuli, interaction between treatments with shade dominating the wound signal). Among them were genes from the PKS (Phytochrome Kinase Substrate) family, which was previously studied for its role in phototropism and leaf positioning. Interestingly, we observed reduced shade suppression of the wounding effect in pks2pks4 double mutants while a PKS4 overexpressing line showed constitutively elevated leaves and was less sensitive to wounding. Our results indicate a trait-specific interrelationship between shade and wounding cues on Arabidopsis leaf growth and positioning. Moreover, we identify PKS genes as integrators of external cues in the control of leaf hyponasty further emphasizing the role of these genes in aerial organ positioning.

Plants face different types of stressful situations without the ability to relocate to favorable environments. For example, increasing plant density reduces access to sunlight as plants start to shade each other. Foliar shading represents a stress that many plants cope with by changing their morphology. This includes elongation of stem-like structures and repositioning of leaves to favor access to unfiltered sunlight. Plants also defend themselves against various pathogens including herbivores. Defense mechanisms include the production of deterrent chemical and morphological adaptations such as stunted growth and downwards leaf repositioning. Here we studied the morphological response of plants when simultaneously facing shade and herbivore stress. When facing both stresses petiole growth was intermediate between the shade-enhanced and wound-repressed response. In contrast, the shade cue overrides the wounding cue leading to a similar upwards leaf repositioning in the combined treatments or in the response to shade alone. Using gene expression analyses and genetics we identified two members of the Phytochrome Kinase Substrate family as playing a signal integration role when plants simultaneously faced both stresses. This contributes to our understanding of the mechanisms underlying plant morphological adaptations when facing multiple stresses.

Light Intensity and Temperature Effect on Salvia yangii (B. T. Drew) Metabolic Profile in vitro

Plant in vitro culture is a feasible system for the testing influence of an environmental factor on the accumulation and chemodiversity of specialized metabolites, especially in medicinal plants. Light and temperature are among the most important factors affecting the physiology of plant organisms but their influence on specific metabolic pathways is not completely understood. Here, we examined the morphogenetic response, photosynthetic pigments content, lipid peroxidation level, DPPH radical scavenging activity, and the production of volatile and non-volatile constituents in Salvia yangii B. T. Drew (syn. Perovskia atriplicifolia Benth.) in vitro cultures kept under different light intensities (70, 130, and 220 μmol m^-2 s^-1) and at two selected temperatures (25 and 30°C). The experiment was continued for 7 months to monitor the changes in the treatment response in time. Phytochemical analysis was performed using chromatographic (GC-MS and UHLPC) and spectrophotometric techniques. The light intensity significantly influenced metabolic response in a non-linear manner, whereas temperature-induced adaptive modifications varied within the long cultivation. Significant differences were noted in the content of carnosic and rosmarinic acid, as well as in several sesquiterpenes (alloaromadendrene, β-caryophyllene, α-humulene). At elevated (30°C) temperature, a trend of differently modulated content of two major antioxidants-rosmarinic acid (RA, a phenylpropanoid pathway derived phenolic acid) and carnosic acid (CA, an abietane diterpenoid) was observed, where RA, but not CA, was depending on the light intensity. At 25°C, both compounds depended on light but in various ways. Among the volatile terpenoid compounds, the influence of light was pronounced, leading to modulation of proportions between individual mono- and sesquiterpenes as well as between hydrocarbon and oxygenated compounds. The study provided new information on the metabolic profile plasticity in S. yangii and added to the existing knowledge on the chemical adaptations in plant species from severe habitats.

Looking beyond the gene network - metabolic and mechanical cell drivers of leaf morphogenesis

The above-ground organs in plants display a rich diversity, yet they grow to characteristic sizes and shapes. Organ morphogenesis progresses through a sequence of key events, which are robustly executed spatiotemporally as an emerging property of intrinsic molecular networks while adapting to various environmental cues. This Review focuses on the multiscale control of leaf morphogenesis. Beyond the list of known genetic determinants underlying leaf growth and shape, we focus instead on the emerging novel mechanisms of metabolic and biomechanical regulations that coordinate plant cell growth non-cell-autonomously. This reveals how metabolism and mechanics are not solely passive outcomes of genetic regulation but play instructive roles in leaf morphogenesis. Such an integrative view also extends to fluctuating environmental cues and evolutionary adaptation. This synthesis calls for a more balanced view on morphogenesis, where shapes are considered from the standpoints of geometry, genetics, energy and mechanics, and as emerging properties of the cellular expression of these different properties.

Integration of Light and Auxin Signaling in Shade Plants: From Mechanisms to Opportunities in Urban Agriculture

With intensification of urbanization throughout the world, food security is being threatened by the population surge, frequent occurrence of extreme climate events, limited area of available cultivated land, insufficient utilization of urban space, and other factors. Determining the means by which high-yielding and high-quality crops can be produced in a limited space is an urgent priority for plant scientists. Dense planting, vertical production, and indoor cultivation are effective ways to make full use of space and improve the crop yield. The results of physiological and molecular analyses of the model plant species Arabidopsis thaliana have shown that the plant response to shade is the key to regulating the plant response to changes in light intensity and quality by integrating light and auxin signals. In this study, we have summarized the major molecular mechanisms of shade avoidance and shade tolerance in plants. In addition, the biotechnological strategies of enhancing plant shade tolerance are discussed. More importantly, cultivating crop varieties with strong shade tolerance could provide effective strategies for dense planting, vertical production, and indoor cultivation in urban agriculture in the future.

A genome‐wide analysis suggests pleiotropic effects of Green Revolution genes on shade avoidance in wheat

A classic example of phenotypic plasticity in plants is the suit of phenotypic responses induced by a change in the ratio of red to far-red light (R∶FR) as a result of shading, also known as the shade avoidance syndrome (SAS). While the adaptive consequences of this syndrome have been extensively discussed in natural ecosystems, how SAS varies within crop populations and how SAS evolved during crop domestication and breeding remain poorly known. In this study, we grew a panel of 180 durum wheat (Triticum turgidum ssp. durum) genotypes spanning diversity from wild, early domesticated, and elite genetic compartments under two light treatments: low R:FR light (shaded treatment) and high R:FR light (unshaded treatment). We first quantified the genetic variability of SAS, here measured as a change in plant height at the seedling stage. We then dissected the genetic basis of this variation through genome-wide association mapping. Genotypes grown in shaded conditions were taller than those grown under unshaded conditions. Interaction between light quality and genotype did not affect plant height. We found six QTLs affecting plant height. Three significantly interacted with light quality among which the well-known Rht1 gene introgressed in elite germplasm during the Green Revolution. Interestingly at three loci, short genotypes systematically expressed reduced SAS, suggesting a positive genetic correlation between plant height and plant height plasticity. Overall, our study sheds light on the evolutionary history of crops and illustrates the relevance of genetic approaches to tackle agricultural challenges.

A PSTAIRE-type cyclin-dependent kinase controls light responses in land plants

Light is a critical signal perceived by plants to adapt their growth rate and direction. Although many signaling components have been studied, how plants respond to constantly fluctuating light remains underexplored. Here, we showed that in the moss Physcomitrium (Physcomitrella) patens, the PSTAIRE-type cyclin-dependent kinase PpCDKA is dispensable for growth. Instead, PpCDKA and its homolog in Arabidopsis thaliana control light-induced tropisms and chloroplast movements by probably influencing the cytoskeleton organization independently of the cell cycle. In addition, lower PpCDKA kinase activity was required to elicit light responses relative to cell cycle regulation. Thus, our study suggests that plant CDKAs may have been co-opted to control multiple light responses, and owing to the bistable switch properties of PSTAIRE-type CDKs, the noncanonical functions are widely conserved for eukaryotic environmental adaptation.

Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling

Phytochrome A (phyA) is the far-red (FR) light photoreceptor in plants that is essential for seedling de-etiolation under FR-rich environments, such as canopy shade. TANDEM ZINC-FINGER/PLUS3 (TZP) was recently identified as a key component of phyA signal transduction in Arabidopsis thaliana; however, how TZP is integrated into the phyA signaling networks remains largely obscure. Here, we demonstrate that ELONGATED HYPOCOTYL5 (HY5), a well-characterized transcription factor promoting photomorphogenesis, mediates FR light induction of TZP expression by directly binding to a G-box motif in the TZP promoter. Furthermore, TZP physically interacts with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), an E3 ubiquitin ligase targeting HY5 for 26S proteasome-mediated degradation, and this interaction inhibits COP1 interaction with HY5. Consistent with those results, TZP post-translationally promotes HY5 protein stability in FR light, and in turn, TZP protein itself is destabilized by COP1 in both dark and FR light conditions. Moreover, tzp hy5 double mutants display an additive phenotype relative to their respective single mutants under high FR light intensities, indicating that TZP and HY5 also function in largely independent pathways. Together, our data demonstrate that HY5 and TZP mutually upregulate each other in transmitting the FR light signal, thus providing insights into the complicated but delicate control of phyA signaling networks.

Mechanism Underlying the Shading-Induced Chlorophyll Accumulation in Tea Leaves

Besides aroma and taste, the color of dry tea leaves, tea infusion, and infused tea leaves is also an important index for tea quality. Shading can significantly increase the chlorophyll content of tea leaves, leading to enhanced tea leaf coloration. However, the underlying regulatory mechanism remains unclear. In this study, we revealed that the expressions of chlorophyll synthesis genes were significantly induced by shading, specially, the gene encoding protochlorophyllide oxidoreductase (CsPOR). Indoor control experiment showed that decreased light intensity could significantly induce the expression of CsPOR, and thus cause the increase of chlorophyll content. Subsequently, we explored the light signaling pathway transcription factors regulating chlorophyll synthesis, including CsPIFs and CsHY5. Through expression level and subcellular localization analysis, we found that CsPIF3-2, CsPIF7-1, and CsHY5 may be candidate transcriptional regulators. Transcriptional activation experiments proved that CsHY5 inhibits CsPORL-2 transcription. In summary, we concluded that shading might promote the expression of CsPORL-2 by inhibiting the expression of CsHY5, leading to high accumulation of chlorophyll in tea leaves. The results of this study provide insights into the mechanism regulating the improvements to tea plant quality caused by shading.

Transcriptome sequencing revealed the influence of blue light on the expression levels of light-stress response genes in Centella asiatica

Centella asiatica is rich in medical and cosmetic properties. While physiological responses of C. asiatica to light have been widely reported, the knowledge of the effects of light on its gene expression is sparse. In this study, we used RNA sequencing (RNA-seq) to investigate the expression of the C. asiatica genes in response to monochromatic red and blue light. Most of the differentially expressed genes (DEGs) under blue light were up-regulated but those under red light were down-regulated. The DEGs encoded for CRY-DASH and UVR3 were among up-regulated genes that play significant roles in responses under blue light. The DEGs involved in the response to photosystem II photodamages and in the biosynthesis of photoprotective xanthophylls were also up-regulated. The expression of flavonoid biosynthetic DEGs under blue light was up-regulated but that under red light was down-regulated. Correspondingly, total flavonoid content under blue light was higher than that under red light. The ABI5, MYB4, and HYH transcription factors appeared as hub nodes in the protein-protein interaction network of the DEGs under blue light while ERF38 was a hub node among the DEGs under red light. In summary, stress-responsive genes were predominantly up-regulated under blue light to respond to stresses that could be induced under high energy light. The information obtained from this study can be useful to better understand the responses of C. asiatica to different light qualities.

Comparative phenotypic and transcriptomic analyses unravel conserved and distinct mechanisms underlying shade avoidance syndrome in Brassicaceae vegetables

Background

Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a reduction in agricultural productivity. Understanding of SAS is crucial for sustainable agricultural practices, especially for high-density indoor farming. Brassicaceae vegetables are widely consumed around the world and are commonly cultivated in indoor farms. However, our understanding of SAS in Brassicaceae vegetables and their genome-wide transcriptional regulatory networks are still largely unexplored.

Results

Shade induced common signs of SAS, including hypocotyl elongation and reduced carotenoids/anthocyanins biosynthesis, in two different Brassicaceae species: Brassica rapa (Choy Sum and Pak Choy) and Brassica oleracea (Kai Lan). Phenotype-assisted transcriptome analysis identified a set of genes induced by shade in these species, many of which were related to auxin biosynthesis and signaling [e.g. YUCCA8 (YUC8), YUC9, and INDOLE-3-ACETIC ACID INDUCIBLE (IAAs)] and other phytohormones signaling pathways including brassinosteroids and ethylene. The genes functioning in plant defense (e.g. MYB29 and JASMONATE-ZIM-DOMAIN PROTEIN 9) as well as in biosynthesis of anthocyanins and glucosinolates were repressed upon shade. Besides, each species also exhibited distinct SAS phenotypes. Shade strongly reduced primary roots and elongated petioles of B. oleracea, Kai Lan. However, these SAS phenotypes were not clearly recognized in B. rapa, Choy Sum and Pak Choy. Some auxin signaling genes (e.g. AUXIN RESPONSE FACTOR 19, IAA10, and IAA20) were specifically induced in B. oleracea, while homologs in B. rapa were not up-regulated under shade. Contrastingly, shade-exposed B. rapa vegetables triggered the ethylene signaling pathway earlier than B. oleracea, Kai Lan. Interestingly, shade induced the transcript levels of LONG HYPOCOTYL IN FAR-RED 1 (HFR1) homolog in only Pak Choy as B. rapa. As HFR1 is a key negative regulator of SAS in Arabidopsis, our finding suggests that Pak Choy HFR1 homolog may also function in conferring higher shade tolerance in this variety.

Conclusions

Our study shows that two Brassicaceae species not only share a conserved SAS mechanism but also exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08076-1.

Rapid adaptive responses of rosette-type macrophyte Vallisneria natans juveniles to varying water depths: The role of leaf trait plasticity

Rosette-type submerged macrophytes are widely distributed across a range of water depths in shallow lakes and play a key role in maintaining ecosystem structures and functions. However, little is known about the rapid adaptive responses of such macrophytes to variations in water depth, especially at the juvenile stage. Here, we conducted a short-term in situ mesocosm experiment, in which the juveniles of Vallisneria natans were exposed to a water depth gradient ranging from 20 to 360 cm. Twenty-two leaf-related traits were examined after 4 weeks of growth in a shallow lake. Most (18) traits of V. natans generally showed high plasticity in relation to water depth. Specifically, juveniles allocated more biomass to leaves and had higher specific leaf area, leaf length-to-width ratio, chlorophyll content, and carotenoids content in deep waters, displaying trait syndrome associated with high resource acquisition. In contrast, V. natans juveniles in shallow waters had higher leaf dry matter content, leaf soluble carbohydrate content, carotenoids per unit chlorophyll, and peroxidase activity, pertaining to resource conservation. Notably, underwater light intensity was found to be the key factor explaining the trait plasticity along the water depth gradient, and 1.30 mol photons m-2 d-1 (at 270 cm) could be the optimal irradiance level based on the total biomass of V. natans juveniles. The present study highlights the significance of leaf trait plasticity for rosette-type macrophytes in response to variations in water depth and sheds new light on the differences between trade-offs in deep- and shallow-water areas.

Phytochrome A elevates plant circadian-clock components to suppress shade avoidance in deep-canopy shade

Shade-avoiding plants can detect the presence of neighboring vegetation and evoke escape responses before canopy cover limits photosynthesis. Rapid stem elongation facilitates light foraging and enables plants to overtop competitors. A major regulator of this response is the phytochrome B photoreceptor, which becomes inactivated in light environments with a low ratio of red to far-red light (low R:FR), characteristic of vegetational shade. Although shade avoidance can provide plants with a competitive advantage in fast-growing stands, excessive stem elongation can be detrimental to plant survival. As such, plants have evolved multiple feedback mechanisms to attenuate shade-avoidance signaling. The very low R:FR and reduced levels of photosynthetically active radiation (PAR) present in deep canopy shade can, together, trigger phytochrome A (phyA) signaling, inhibiting shade avoidance and promoting plant survival when resources are severely limited. The molecular mechanisms underlying this response have not been fully elucidated. Here, we show that Arabidopsis thaliana phyA elevates early-evening expression of the central circadian-clock components TIMING OF CAB EXPRESSION 1 (TOC1), PSEUDO RESPONSE REGULATOR 7 (PRR7), EARLY FLOWERING 3 (ELF3), and ELF4 in photocycles of low R:FR and low PAR. These collectively suppress stem elongation, antagonizing shade avoidance in deep canopy shade.