Lights, location, action: Shade avoidance signalling over spatial scales

Plants growing in dense vegetation stands need to flexibly position their photosynthetic organs to ensure optimal light capture in a competitive environment. They do so through a suite of developmental responses referred to as the shade avoidance syndrome. Belowground, root development is also adjusted in response to aboveground neighbour proximity. Canopies are dynamic and complex environments with heterogenous light cues in the far-red, red, blue and UV spectrum, which can be perceived with photoreceptors by spatially separated plant tissues. Molecular regulation of plant architecture adjustment via PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factors and growth-related hormones such as auxin, gibberellic acid, brassinosteroids and abscisic acid were historically studied without much attention to spatial or tissue-specific context. Recent developments and technologies have, however, sparked strong interest in spatially explicit understanding of shade avoidance regulation. Other environmental factors such as temperature and nutrient availability interact with the molecular shade avoidance regulation network, often depending on the spatial location of the signals, and the responding organs. Here, we aim to review recent advances in how plants respond to heterogenous light cues and integrate these with other environmental signals.

A tomato B-box protein regulates plant development and fruit quality through the interaction with PIF4, HY5 and RIN transcription factors

During the last decade, the knowledge about BBX proteins has abruptly increased. Genome-wide studies identified BBX gene family in several ornamental, industry and food crops; however, the reports regarding the role of these genes as regulators of agronomically important traits are scarce. Here, by phenotyping a knockout mutant, we performed a comprehensive functional characterization of the tomato locus Solyc12g089240, hereafter called SlBBX20. The data revealed the encoded protein as a positive regulator of light signaling affecting several physiological processes during plant lifespan. By the inhibition of PHYTOCHROME INTERACTING FACTOR 4 (SlPIF4)-auxin crosstalk, SlBBX20 regulates photomorphogenesis. Later, it controls the balance between cell division and expansion to guarantee the correct vegetative and reproductive development. In fruits, SlBBX20 is transcriptionally induced by the master transcription factor RIPENING INHIBITOR (SlRIN) and, together with ELONGATED HYPOCOTYL 5 (SlHY5), upregulates flavonoids biosynthetic genes. Finally, SlBBX20 promotes the accumulation of steroidal glycoalkaloids and attenuates Botrytis cinerea infection. This work clearly demonstrates that BBX proteins are multilayer regulators of plant physiology, not only because they affect multiple processes along plant development but also regulate other genes at the transcriptional and post-translational levels.

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.

Effects of far-red light on the behaviour and reproduction of the zoophytophagous predator Macrolophus pygmaeus and its interaction with a whitefly herbivore

Plants can detect neighbouring plants through a reduction in the ratio between red and far-red light (R:FR). This provides a signal of plant-plant competition and induces rapid plant growth while inhibiting defence against biotic stress, two interlinked responses designated as the shade avoidance syndrome (SAS). Consequently, the SAS can influence plant-herbivore interactions that could cascade to higher trophic levels. However, little is known about how the expression of the SAS can influence tritrophic interactions. We investigated whether changes in R:FR affect the emission of herbivore-induced plant volatiles (HIPVs), and whether these changes influence the attraction of the zoophytophagous predator Macrolophus pygmaeus. We also studied how the expression of the SAS and subsequent inhibition of plant defences affects the reproduction of M. pygmaeus in both the presence and absence of the greenhouse whitefly (WF) (Trialeurodes vaporariorum) as arthropod prey. The results show that changes in R:FR have little effect on HIPV emissions and predator attraction. However, a reduction in R:FR leads to increased reproduction of both the predator and the WFs. We discuss that shade avoidance responses can increase the population development of M. pygmaeus through a combination of reduced plant defences and increased herbivore densities.

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.

Molecular mechanisms of shade tolerance in plants

Shade tolerance is an ecological concept used in a wide range of disciplines, from plant physiology to landscaping or gardening. It refers to the strategy of some plants to persist and even thrive in environments with low light levels because of the shade produced by the vegetation proximity (e.g. in the understory). Shade tolerance influences the organization, structure, functioning, and dynamics of plant communities. However, little is known about its molecular and genetic basis. By contrast, there is a good understanding on how plants deal with the proximity of other plants, a divergent strategy used by most crops to respond to vegetation proximity. While generally shade-avoiding species strongly elongate in response to the proximity of other plants, shade-tolerant species do not. Here we review the molecular mechanisms that control the regulation of hypocotyl elongation in shade-avoiding species as a reference framework to understand shade tolerance. Comparative studies indicate that shade tolerance is implemented by components also known to regulate hypocotyl elongation in shade-avoiding species. These components, however, show differential molecular properties that explain how, in response to the same stimulus, shade-avoiding species elongate while shade-tolerant ones do not.

On the contrasting morphological response to far-red at high and low photon fluxes

Plants compete for sunlight and have evolved to perceive shade through both relative increases in the flux of far-red photons (FR; 700 to 750 nm) and decreases in the flux of all photons (intensity). These two signals interact to control stem elongation and leaf expansion. Although the interacting effects on stem elongation are well quantified, responses for leaf expansion are poorly characterized. Here we report a significant interaction between far-red fraction and total photon flux. Extended photosynthetic photon flux density (ePPFD; 400 to 750 nm) was maintained at three levels (50/100, 200 and 500 µmol m^-2 s^-1), each with a range of 2 to 33% FR. Increasing FR increased leaf expansion in three cultivars of lettuce at the highest ePPFD but decreased expansion at the lowest ePPFD. This interaction was attributed to differences in biomass partitioning between leaves and stems. Increased FR favored stem elongation and biomass partitioning to stems at low ePPFD and favored leaf expansion at high ePPFD. In cucumber, leaf expansion was increased with increasing percent FR under all ePPFD levels showing minimal interaction. The interactions (and lack thereof) have important implications for horticulture and warrant further study for plant ecology.

Light and jasmonic acid coordinately regulate the phosphate responses under shade and phosphate starvation conditions in Arabidopsis

In the natural ecosystem, plants usually grow at high vegetation density for yield maximization. The high-density planting triggers a variety of strategies to avoid canopy shade and competes with their neighbors for light and nutrition, which are collected termed shade avoidance responses. The molecular mechanism underlying shade avoidance and nutrition has expanded largely in the past decade; however, how these two responses intersect remains poorly understood. Here, we show that simulated shade undermined Pi starvation response and the phytohormone JA is involved in this process. We found that the JA signaling repressor JAZ proteins directly interact with PHR1 to repress its transcriptional activity on downstream targets, including phosphate starvation induced genes. Furthermore, FHY3 and FAR1, the negative regulators of shade avoidance, directly bind to promoters of NIGT1.1 and NIGT1.2 to activate their expression, and this process is also antagonized by JAZ proteins. All these results finally result in attenuation of Pi starvation response under shade and Pi-depleted conditions. Our findings unveil a previously unrecognized molecular framework whereby plants integrate light and hormone signaling to modulate phosphate responses under plant competition.

PIF7-mediated epigenetic reprogramming promotes the transcriptional response to shade in Arabidopsis

For shade-intolerant plants, changes in light quality through competition from neighbors trigger shade avoidance syndrome (SAS): a series of morphological and physiological adaptations that are ultimately detrimental to plant health and crop yield. Phytochrome-interacting factor 7 (PIF7) is a major transcriptional regulator of SAS in Arabidopsis; however, how it regulates gene expression is not fully understood. Here, we show that PIF7 directly interacts with the histone chaperone anti-silencing factor 1 (ASF1). The ASF1-deprived asf1ab mutant showed defective shade-induced hypocotyl elongation. Histone regulator homolog A (HIRA), which mediates deposition of the H3.3 variant into chromatin, is also involved in SAS. RNA/ChIP-sequencing analyses identified the role of ASF1 in the direct regulation of a subset of PIF7 target genes. Furthermore, shade-elicited gene activation is accompanied by H3.3 enrichment, which is mediated by the PIF7-ASF1-HIRA regulatory module. Collectively, our data reveal that PIF7 recruits ASF1-HIRA to increase H3.3 incorporation into chromatin to promote gene transcription, thus enabling plants to effectively respond to environmental shade.

Meristem dormancy in Marchantia polymorpha is regulated by a liverwort-specific miRNA and a clade III SPL gene

The shape of modular organisms depends on the branching architecture, which in plants is determined by the fates of generative centers called meristems. The branches of the liverwort Marchantia polymorpha are derived from two adjacent meristems that develop at thallus apices. These meristems may be active and develop branches or may be dormant and do not form branches. The relative number and position of active and dormant meristems define the overall shape and form of the thallus. We show that the clade III SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor MpSPL1 is required for meristem dormancy. The activity of MpSPL1 is regulated by the liverwort-specific Mpo-MR13 miRNA, which, in turn, is regulated by PIF-mediated signaling. An unrelated PIF-regulated miRNA, MIR156, represses a different SPL gene (belonging to clade IV) that inhibits branching during the shade avoidance response in Arabidopsis thaliana. This suggests that a conserved light signaling mechanism modulates branching architecture in liverworts and angiosperms and therefore is likely operated in the last common ancestor. However, PIF-mediated signaling represses the expression of different miRNA genes with different SPL targets during dichotomous, apical branching in liverworts and during lateral, subapical branching in angiosperms. We speculate that the mechanism that acts downstream of light and regulates meristem dormancy evolved independently in liverworts and angiosperms.

Local light signaling at the leaf tip drives remote differential petiole growth through auxin-gibberellin dynamics

Although plants are immobile, many of their organs are flexible to move in response to environmental cues. In dense vegetation, plants detect neighbors through far-red light perception with their leaf tip. They respond remotely, with asymmetrical growth between the abaxial and adaxial sides of the leafstalk, the petiole. This results in upward movement that brings the leaf blades into better lit zones of the canopy. The plant hormone auxin is required for this response, but it is not understood how non-differential leaf tip-derived auxin can remotely regulate movement. Here, we show that remote signaling of far-red light promotes auxin accumulation in the abaxial petiole. This local auxin accumulation is facilitated by reinforcing an intrinsic directionality of the auxin transport protein PIN3 on the petiole endodermis, as visualized with a PIN3-GFP line. Using an auxin biosensor, we show that auxin accumulates in all cell layers from endodermis to epidermis in the abaxial petiole, upon far-red light signaling in the remote leaf tip. In the petiole, auxin elicits a response to both auxin itself as well as a second growth promoter; gibberellin. We show that this dual regulation is necessary for hyponastic leaf movement in response to light. Our data indicate that gibberellin is required to permit cell growth, whereas differential auxin accumulation determines which cells can grow. Our results reveal how plants can spatially relay information about neighbor proximity from their sensory leaf tips to the petiole base, thus driving adaptive growth.

HFR1, a bHLH Transcriptional Regulator from Arabidopsis thaliana, Improves Grain Yield, Shade and Osmotic Stress Tolerances in Common Wheat

Common wheat, Triticum aestivum, is the most widely grown staple crop worldwide. To catch up with the increasing global population and cope with the changing climate, it is valuable to breed wheat cultivars that are tolerant to abiotic or shade stresses for density farming. Arabidopsis LONG HYPOCOTYL IN FAR-RED 1 (AtHFR1), a photomorphogenesis-promoting factor, is involved in multiple light-related signaling pathways and inhibits seedling etiolation and shade avoidance. We report that overexpression of AtHFR1 in wheat inhibits etiolation phenotypes under various light and shade conditions, leading to shortened plant height and increased spike number relative to non-transgenic plants in the field. Ectopic expression of AtHFR1 in wheat increases the transcript levels of TaCAB and TaCHS as observed previously in Arabidopsis, indicating that the AtHFR1 transgene can activate the light signal transduction pathway in wheat. AtHFR1 transgenic seedlings significantly exhibit tolerance to osmotic stress during seed germination compared to non-transgenic wheat. The AtHFR1 transgene represses transcription of TaFT1, TaCO1, and TaCO2, delaying development of the shoot apex and heading in wheat. Furthermore, the AtHFR1 transgene in wheat inhibits transcript levels of PHYTOCHROME-INTERACTING FACTOR 3-LIKEs (TaPIL13, TaPIL15-1B, and TaPIL15-1D), downregulating the target gene STAYGREEN (TaSGR), and thus delaying dark-induced leaf senescence. In the field, grain yields of three AtHFR1 transgenic lines were 18.2–48.1% higher than those of non-transgenic wheat. In summary, genetic modification of light signaling pathways using a photomorphogenesis-promoting factor has positive effects on grain yield due to changes in plant architecture and resource allocation and enhances tolerances to osmotic stress and shade avoidance response.

Organ-specific COP1 control of BES1 stability adjusts plant growth patterns under shade or warmth

Under adverse conditions such as shade or elevated temperatures, cotyledon expansion is reduced and hypocotyl growth is promoted to optimize plant architecture. The mechanisms underlying the repression of cotyledon cell expansion remain unknown. Here, we report that the nuclear abundance of the BES1 transcription factor decreased in the cotyledons and increased in the hypocotyl in Arabidopsis thaliana under shade or warmth. Brassinosteroid levels did not follow the same trend. PIF4 and COP1 increased their nuclear abundance in both organs under shade or warmth. PIF4 directly bound the BES1 promoter to enhance its activity but indirectly reduced BES1 expression. COP1 physically interacted with the BES1 protein, promoting its proteasome degradation in the cotyledons. COP1 had the opposite effect in the hypocotyl, demonstrating organ-specific regulatory networks. Our work indicates that shade or warmth reduces BES1 activity by transcriptional and post-translational regulation to inhibit cotyledon cell expansion.

Integrated Expression Analysis of Small RNA, Degradome and Microarray Reveals Complex Regulatory Action of miRNA during Prolonged Shade in Swarnaprabha Rice

Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade.

Induced Mutation in GmCOP1b Enhances the Performance of Soybean under Dense Planting Conditions

CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) is the key photomorphogenic inhibitor that has been extensively studied in higher plants. Nevertheless, its role has not been documented in the economically important soybean. Here we investigated the functions of two COP1 homologous genes, GmCOP1a and GmCOP1b, by analyzing Gmcop1a and Gmcop1b mutants with indels using CRISPR in soybean. We revealed that, although both genes are required for skotomorphogenesis in the dark, the GmCOP1b gene seems to play a more prominent role than GmCOP1a in promoting stem elongation under normal light conditions. Consistently, the bZIP transcriptional factors STF1/2, which repress stem elongation in soybean, accumulated to the highest level in the Gmcop1a1b double mutant, followed by the Gmcop1b and Gmcop1a mutants. Furthermore, the Gmcop1b mutants showed reduced shade response and enhanced performance under high-density conditions in field trials. Taken together, this study provides essential genetic resources for elucidating functional mechanisms of GmCOP1 and breeding of high yield soybean cultivars for future sustainable agriculture.

INTERMEDIUM-C mediates the shade-induced bud growth arrest in barley

Tiller formation is a key agronomic determinant for grain yield in cereal crops. The modulation of this trait is controlled by transcriptional regulators and plant hormones, tightly regulated by external environmental conditions. While endogenous (genetic) and exogenous (environmental factors) triggers for tiller formation have mostly been investigated separately, it has remained elusive how they are integrated into the developmental program of this trait. The transcription factor gene INTERMEDIUM-C (INT-C), which is the barley ortholog of the maize domestication gene TEOSINTE BRANCHED1 (TB1), has a prominent role in regulating tiller bud outgrowth. Here we show that INT-C is expressed in tiller buds, required for bud growth arrest in response to shade. In contrast to wild-type plants, int-c mutant plants are impaired in their shade response and do not stop tiller production after shading. Gene expression levels of INT-C are up-regulated under light-limiting growth conditions, and down-regulated after decapitation. Transcriptome analysis of wild-type and int-c buds under control and shading conditions identified target genes of INT-C that belong to auxin and gibberellin biosynthesis and signaling pathways. Our study identifies INT-C as an integrator of the shade response into tiller formation, which is prerequisite for implementing shading responses in the breeding of cereal crops.

Effects of Green Light on Elongation Do Not Interact with Far-Red, Unless the Phytochrome Photostationary State (PSS) Changes in Tomato

Simple Summary

This paper focuses on the role of phytochromes (phys) in the interaction between green light and far-red light effects on “shade avoidance syndrome”. We grew wild type and phy mutants of tomato under a set of light conditions with different combinations of green, blue, red, and far-red light. Partial (20%) replacement of red/blue by green light in the absence of far-red light hardly affected the tomato plant morphology. However, when the spectrum contained far-red light, partially replacing red/blue by green light resulted in more elongation, which was associated with a lower phytochrome photostationary state (PSS) value. There was no effect of partial substitution of red/blue with green light when the PSS was kept constant. Thus, this study has revealed an interaction between green and far-red light effects on elongation unless PSS was kept constant. Green light was often a bit neglected in photobiology, but now an increasing number of researchers are realizing that green light deserves more attention. This study advances the understanding of light quality and plant growth and finding the optimal spectrum when growing plants under LED lighting in controlled environment agriculture.

Abstract

Green light (G) could trigger a “shade avoidance syndrome” (SAS) similarly to far-red light. We aimed to test the hypothesis that G interacts with far-red light to induce SAS, with this interaction mediated by phytochromes (phys). The tomato (Solanum lycopersicum cv. Moneymaker) wild-type (WT) and phyA, phyB1B2, and phyAB1B2 mutants were grown in a climate room with or without 30 µmol m⁻² s⁻¹ G on red/blue and red/blue/far-red backgrounds, maintaining the same photosynthetically active radiation (400–700 nm) of 150 µmol m⁻² s⁻¹ and red/blue ratio of 3. G hardly affected the dry mass accumulation or leaf area of WT, phyA, and phyB1B2 with or without far-red light. A lower phytochrome photostationary state (PSS) by adding far-red light significantly increased the total dry mass by enhancing the leaf area in WT plants but not in phy mutants. When the background light did not contain far-red light, partially replacing red/blue with G did not significantly affect stem elongation. However, when the background light contained far-red light, partially replacing red/blue with G enhanced elongation only when associated with a decrease in PSS, indicating that G interacts with far-red light on elongation only when the PSS changes.

Understanding the Shade Tolerance Responses Through Hints From Phytochrome A-Mediated Negative Feedback Regulation in Shade Avoiding Plants

Based on how plants respond to shade, we typically classify them into two groups: shade avoiding and shade tolerance plants. Under vegetative shade, the shade avoiding species induce a series of shade avoidance responses (SARs) to outgrow their competitors, while the shade tolerance species induce shade tolerance responses (STRs) to increase their survival rates under dense canopy. The molecular mechanism underlying the SARs has been extensively studied using the shade avoiding model plant Arabidopsis thaliana, while little is known about STRs. In Aarabidopsis, there is a PHYA-mediated negative feedback regulation that suppresses exaggerated SARs. Recent studies revealed that in shade tolerance Cardamine hirsuta plants, a hyperactive PHYA was responsible for suppressing shade-induced elongation growth. We propose that similar signaling components may be used by shade avoiding and shade tolerance plants, and different phenotypic outputs may result from differential regulation or altered dynamic properties of these signaling components. In this review, we summarized the role of PHYA and its downstream components in shade responses, which may provide insights into understanding how both types of plants respond to shade.

Phytochrome B and PHYTOCHROME INTERACTING FACTOR8 modulate seasonal growth in trees

The seasonally synchronized annual growth cycle that is regulated mainly by photoperiod and temperature cues is a crucial adaptive strategy for perennial plants in boreal and temperate ecosystems. Phytochrome B (phyB), as a light and thermal sensor, has been extensively studied in Arabidopsis. However, the specific mechanisms for how the phytochrome photoreceptors control the phenology in tree species remain poorly understood. We characterized the functions of PHYB genes and their downstream PHYTOCHROME INTERACTING FACTOR (PIF) targets in the regulation of shade avoidance and seasonal growth in hybrid aspen trees. We show that while phyB1 and phyB2, as phyB in other plants, act as suppressors of shoot elongation during vegetative growth, they act as promoters of tree seasonal growth. Furthermore, while the Populus homologs of both PIF4 and PIF8 are involved in the shade avoidance syndrome (SAS), only PIF8 plays a major role as a suppressor of seasonal growth. Our data suggest that the PHYB-PIF8 regulon controls seasonal growth through the regulation of FT and CENL1 expression while a genome-wide transcriptome analysis suggests how, in Populus trees, phyB coordinately regulates SAS responses and seasonal growth cessation.

Functional convergence of growth responses to shade and warmth in Arabidopsis

Shade and warmth promote the growth of the stem, but the degree of mechanistic convergence and functional association between these responses is not clear. We analysed the quantitative impact of mutations and natural genetic variation on the hypocotyl growth responses of Arabidopsis thaliana to shade and warmth, the relationship between the abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and growth stimulation by shade or warmth, the effects of both cues on the transcriptome and the consequences of warm temperature on carbon balance. Growth responses to shade and warmth showed strong genetic linkage and similar dependence on PIF4 levels. Temperature increased growth and phototropism even within a range where damage by extreme high temperatures is unlikely to occur in nature. Both cues enhanced the expression of growth-related genes and reduced the expression of photosynthetic genes. However, only warmth enhanced the expression of genes involved in responses to heat. Warm temperatures substantially increased the amount of light required to compensate for the daily carbon dioxide balance. We propose that the main ecological function of hypocotyl growth responses to warmth is to increase the access of shaded photosynthetic organs to light, which implies functional convergence with shade avoidance.

Evolution of shade tolerance is associated with attenuation of shade avoidance and reduced phenotypic plasticity in North American milkweeds

PREMISE

Mismatches between light conditions and light-capture strategy can reduce plant performance and prevent colonization of novel habitats. Although light-capture strategies tend to be highly conserved among closely related species, evolutionary transitions from shaded to unshaded habitats (and vice versa) occur in numerous plant lineages.

METHODS

We combined phylogenetic approaches with field and greenhouse experiments to investigate evolutionary constraints on light-capture strategy in North American milkweeds (genus Asclepias) and to determine whether colonization of shaded habitats in this heliophilic clade is associated with reduced plasticity and attenuation of the shade avoidance response.

RESULTS

Colonization of shaded habitats has occurred at least 10 times in this genus, including at least once in each major North American clade. Evolutionary transitions between habitats exhibit strong directional bias, with shifts from full-sun to shaded habitats occurring at least three times as often as the opposite transition. In field and greenhouse experiments, sun species responded to shade by increasing internode length, height, and specific leaf area, consistent with the shade avoidance response; paired shade species exhibited reduced plasticity overall, and only one trait (specific leaf area) responded to experimental shade.

CONCLUSIONS

Our results suggest that milkweeds colonized shaded environments multiple times using a light-capture strategy distinct from the ancestral (putatively shade avoidant) strategy, including a general attenuation of plasticity in response to variable light conditions. This pattern bolsters the notion that shade avoidance and tolerance represent divergent evolutionary strategies for maximizing performance under qualitatively different types of shade.

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.

Phytochrome B links the environment to transcription

Phytochrome B (phyB) senses the difference between darkness and light, the level of irradiance, the red/far-red ratio, and temperature. Thanks to these sensory capacities, phyB perceives whether plant organs are buried in the soil, exposed to full sunlight, in the presence of nearby vegetation, and/or under risk of heat stress. In some species, phyB perceives seasonal daylength cues. phyB affects the activity of several transcriptional regulators either by direct physical interaction or indirectly by physical interaction with proteins involved in the turnover of transcriptional regulators. Typically, interaction of a protein with phyB has either negative or positive effects on the interaction of the latter with a third party, this being another protein or DNA. Thus, phyB mediates the context-dependent modulation of the transcriptome underlying changes in plant morphology, physiology, and susceptibility to biotic and abiotic stress. phyB operates as a dynamic switch that improves carbon balance, prioritizing light interception and photosynthetic capacity in open places and the projection of the shoot towards light in the soil, under shade and in warm conditions.

Reducing shade avoidance can improve Arabidopsis canopy performance against competitors

Plants that grow in high density communities activate shade avoidance responses to consolidate light capture by individuals. Although this is an evolutionary successful strategy, it may not enhance performance of the community as a whole. Resources are invested in shade responses at the expense of other organs and light penetration through the canopy is increased, allowing invading competitors to grow better. Here we investigate if suppression of shade avoidance responses would enhance group performance of a monoculture community that is invaded by a competitor. Using different Arabidopsis genotypes, we show that suppression of shade-induced upward leaf movement in the pif7 mutant increases the pif7 communal performance against invaders as compared to a wild-type canopy. The invaders were more severely suppressed and the community grew larger as compared to wild type. Using computational modelling, we show that leaf angle variations indeed strongly affect light penetration and growth of competitors that invade the canopy. Our data thus show that modifying specific shade avoidance aspects can improve plant community performance. These insights may help to suppress weeds in crop stands.

Regulation of Lateral Root Development by Shoot-Sensed Far-Red Light via HY5 Is Nitrate-Dependent and Involves the NRT2.1 Nitrate Transporter

Plants are very effective in responding to environmental changes during competition for light and nutrients. Low Red:Far-Red (low R:FR)-mediated neighbor detection allows plants to compete successfully with other plants for available light. This above-ground signal can also reduce lateral root growth by inhibiting lateral root emergence, a process that might help the plant invest resources in shoot growth. Nitrate is an essential nutrient for plant growth and Arabidopsis thaliana responds to low nitrate conditions by enhancing nutrient uptake and reducing lateral and main root growth. There are indications that low R:FR signaling and low nitrate signaling can affect each other. It is unknown which response is prioritized when low R:FR light- and low nitrate signaling co-occur. We investigated the effect of low nitrate conditions on the low R:FR response of the A. thaliana root system in agar plate media, combined with the application of supplemental Far-Red (FR) light to the shoot. We observed that under low nitrate conditions main and lateral root growth was reduced, but more importantly, that the response of the root system to low R:FR was not present. Consistently, a loss-of-function mutant of a nitrate transporter gene NRT2.1 lacked low R:FR-induced lateral root reduction and its root growth was hypersensitive to low nitrate. ELONGATED HYPOCOTYL5 (HY5) plays an important role in the root response to low R:FR and we found that it was less sensitive to low nitrate conditions with regards to lateral root growth. In addition, we found that low R:FR increases NRT2.1 expression and that low nitrate enhances HY5 expression. HY5 also affects NRT2.1 expression, however, it depended on the presence of ammonium in which direction this effect was. Replacing part of the nitrogen source with ammonium also removed the effect of low R:FR on the root system, showing that changes in nitrogen sources can be crucial for root plasticity. Together our results show that nitrate signaling can repress low R:FR responses and that this involves signaling via HY5 and NRT2.1.

Phenotypic Response to Light Versus Shade Associated with DNA Methylation Changes in Snapdragon Plants (Antirrhinum majus)

The phenotypic plasticity of plants in response to change in their light environment, and in particularly, to shade is a schoolbook example of ecologically relevant phenotypic plasticity with evolutionary adaptive implications. Epigenetic variation is known to potentially underlie plant phenotypic plasticity. Yet, little is known about its role in ecologically and evolutionary relevant mechanisms shaping the diversity of plant populations in nature. Here we used a reference-free reduced representation bisulfite sequencing method for non-model organisms (epiGBS) to investigate changes in DNA methylation patterns across the genome in snapdragon plants (Antirrhinum majus L.). We exposed plants to sunlight versus artificially induced shade in four highly inbred lines to exclude genetic confounding effects. Our results showed that phenotypic plasticity in response to light versus shade shaped vegetative traits. They also showed that DNA methylation patterns were modified under light versus shade, with a trend towards global effects over the genome but with large effects found on a restricted portion. We also detected the existence of a correlation between phenotypic and epigenetic variation that neither supported nor rejected its potential role in plasticity. While our findings imply epigenetic changes in response to light versus shade environments in snapdragon plants, whether these changes are directly involved in the phenotypic plastic response of plants remains to be investigated. Our approach contributed to this new finding but illustrates the limits in terms of sample size and statistical power of population epigenetic approaches in non-model organisms. Pushing this boundary will be necessary before the relationship between environmentally induced epigenetic changes and phenotypic plasticity is clarified for ecologically relevant mechanisms with evolutionary implications.

GmCRY1s modulate gibberellin metabolism to regulate soybean shade avoidance in response to reduced blue light

Soybean is an important legume crop that displays the classic shade avoidance syndrome (SAS), including exaggerated stem elongation, which leads to lodging and yield reduction under density farming conditions. Here, we compared the effects of two shade signals, low red light to far-red light ratio (R:FR) and low blue light (LBL), on soybean status and revealed that LBL predominantly induces excessive stem elongation. We used CRISPR-Cas9-engineered Gmcry mutants to investigate the functions of seven cryptochromes (GmCRYs) in soybean and found that the four GmCRY1s overlap in mediating LBL-induced SAS. Light-activated GmCRY1s increase the abundance of the bZIP transcription factors STF1 and STF2, which directly upregulate the expression of genes encoding GA2 oxidases to deactivate GA1 and repress stem elongation. Notably, GmCRY1b overexpression lines displayed multiple agronomic advantages over the wild-type control under both dense planting and intercropping conditions. Our study demonstrates the integration of GmCRY1-mediated signals with the GA metabolic pathway in the regulation of LBL-induced SAS in soybean. It also provides a promising option for breeding lodging-resistant, high-yield soybean cultivars in the future.

LED Lighting Strategies Affect Physiology and Resilience to Pathogens and Pests in Eggplant (Solanum melongena L.)

Over the last decade, LED lighting has gained considerable interest as an energy-efficient supplemental light source in greenhouse horticulture that can change rapidly in intensity and spectral composition. Spectral composition not only affects crop physiology but may also affect the biology of pathogens, pests, and their natural enemies, both directly and indirectly through an impact on induced plant resistance. In this study, we investigated the effects of light spectrum against a background of sunlight on growth and development of Solanum melongena. These effects were related to the spectral effects on the establishment of populations of the predatory mite Amblyseius swirskii and plant resilience against the biotrophic fungus powdery mildew, the necrotrophic fungus botrytis, and the herbivorous arthropod Western flower thrips. The effects of a reduced red/far-red (R:FR) ratio were studied under two ratios of red to blue light. Far-red light either was supplied additionally to the photosynthetic photon flux density (PPFD) or partially replaced PPFD, while maintaining total photon flux density (PFD). Effects of white light or additional UV-B light on plant resilience was tested, compared to the reference (5% blue, 5% green, and 90% red light). Plant biomass in the vegetative phase increased when additional far-red light was supplied. Stem length increased with far-red, irrespective of PPFD and the percentage of blue light. In the generative phase, total shoot biomass and fruit fresh weights were higher under additional far-red light, followed by the treatments where far-red partly replaced PPFD. Far-red light increased biomass partitioning into the fruits, at the expense of the leaves. There were no differences in population growth of A. swirskii mites between light treatments, nor did light treatment have an effect on the vertical distribution of these predatory mites in the plants. The treatments with additional far-red light reduced the infection rate of powdery mildew, but increased botrytis infection. These differences might be due to the plant defenses acting against these pathogens evolving from two different regulatory pathways. These results show that positive effects of altered spectral compositions on physiological responses were only moderately compensated by increased susceptibility to fungal pathogens, which offers perspective for a sustainable greenhouse horticulture.

Adjustment of the PIF7-HFR1 transcriptional module activity controls plant shade adaptation

Shade caused by the proximity of neighboring vegetation triggers a set of acclimation responses to either avoid or tolerate shade. Comparative analyses between the shade-avoider Arabidopsis thaliana and the shade-tolerant Cardamine hirsuta revealed a role for the atypical basic-helix-loop-helix LONG HYPOCOTYL IN FR 1 (HFR1) in maintaining the shade tolerance in C. hirsuta, inhibiting hypocotyl elongation in shade and constraining expression profile of shade-induced genes. We showed that C. hirsuta HFR1 protein is more stable than its A. thaliana counterpart, likely due to its lower binding affinity to CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), contributing to enhance its biological activity. The enhanced HFR1 total activity is accompanied by an attenuated PHYTOCHROME INTERACTING FACTOR (PIF) activity in C. hirsuta. As a result, the PIF-HFR1 module is differently balanced, causing a reduced PIF activity and attenuating other PIF-mediated responses such as warm temperature-induced hypocotyl elongation (thermomorphogenesis) and dark-induced senescence. By this mechanism and that of the already-known of phytochrome A photoreceptor, plants might ensure to properly adapt and thrive in habitats with disparate light amounts.

The neonicotinoid insecticide thiamethoxam enhances expression of stress-response genes in Zea mays in an environmentally specific pattern

Recent studies indicate that thiamethoxam (TMX), a neonicotinoid insecticide, can affect plant responses to environmental stressors, such as neighboring weeds. The molecular mechanisms behind both stable and environmentally specific responses to TMX likely involve genes related to defense and stress responses. We investigated the effect of a TMX seed treatment on global gene expression in maize coleoptiles both under normal conditions and under low ratio red to far-red (R:FR) light stress induced by the presence of neighboring plants. The neighboring plant treatment upregulated genes involved in biotic and abiotic stress responses and affected specific photosynthesis and cell-growth related genes. Low R:FR light may enhance maize resistance to herbivores and pathogens. TMX appears to compromise resistance. The TMX treatment stably repressed many genes that encode proteins involved in biotic stress responses, as well as cell-growth genes. Notably, TMX effects on many genes' expression were conditional on the environment. In response to low R:FR, plants treated with TMX engage genes in the JA pathway, as well as other stress-related response pathways. Neighboring weeds may condition TMX-treated plants to become more stress tolerant.

Multiple Loci Control Variation in Plasticity to Foliar Shade Throughout Development in Arabidopsis thaliana

The shade avoidance response is a set of developmental changes exhibited by plants to avoid shading by competitors, and is an important model of adaptive plant plasticity. While the mechanisms of sensing shading by other plants are well-known and appear conserved across plants, less is known about the developmental mechanisms that result in the diverse array of morphological and phenological responses to shading. This is particularly true for traits that appear later in plant development. Here we use a nested association mapping (NAM) population of Arabidopsis thaliana to decipher the genetic architecture of the shade avoidance response in late-vegetative and reproductive plants. We focused on four traits: bolting time, rosette size, inflorescence growth rate, and inflorescence size, found plasticity in each trait in response to shade, and detected 17 total QTL; at least one of which is a novel locus not previously identified for shade responses in Arabidopsis. Using path analysis, we dissected each colocalizing QTL into direct effects on each trait and indirect effects transmitted through direct effects on earlier developmental traits. Doing this separately for each of the seven NAM populations in each environment, we discovered considerable heterogeneity among the QTL effects across populations, suggesting allelic series at multiple QTL or interactions between QTL and the genetic background or the environment. Our results provide insight into the development and variation in shade avoidance responses in Arabidopsis, and emphasize the value of directly modeling the relationships among traits when studying the genetics of complex developmental syndromes.

PIFs coordinate shade avoidance by inhibiting auxin repressor ARF18 and metabolic regulator QQS

Shade avoidance syndrome (SAS) arises in densely growing plants that compete for light. In Arabidopsis thaliana, phytochrome interacting factor (PIF) proteins link the perception of shade to stem elongation via auxin production. Here, we report that PIFs inhibit the shade-induced expression of AUXIN RESPONSE FACTOR 18 (ARF18), and ARF18 represses auxin signaling. Therefore, PIF-mediated inhibition of ARF18 enhances auxin-dependent hypocotyl elongation in simulated shade. Furthermore, we show that both PIFs and ARF18 directly repress qua-quine starch (QQS), which controls the allocation of carbon and nitrogen. Shade-repressed QQS attenuates the conversion of starch to protein and thus reduced leaf area. Our results suggest that PIF-dependent gene regulation coordinates multiple SAS responses, including altered stem growth via ARF18, as well as altered leaf growth and metabolism via QQS.

Photoreceptors Regulate Plant Developmental Plasticity through Auxin

Light absorption by plants changes the composition of light inside vegetation. Blue (B) and red (R) light are used for photosynthesis whereas far-red (FR) and green light are reflected. A combination of UV-B, blue and R:FR-responsive photoreceptors collectively measures the light and temperature environment and adjusts plant development accordingly. This developmental plasticity to photoreceptor signals is largely regulated through the phytohormone auxin. The phytochrome, cryptochrome and UV Resistance Locus 8 (UVR8) photoreceptors are inactivated in shade and/or elevated temperature, which releases their repression of Phytochrome Interacting Factor (PIF) transcription factors. Active PIFs stimulate auxin synthesis and reinforce auxin signalling responses through direct interaction with Auxin Response Factors (ARFs). It was recently discovered that shade-induced hypocotyl elongation and petiole hyponasty depend on long-distance auxin transport towards target cells from the cotyledon and leaf tip, respectively. Other responses, such as phototropic bending, are regulated by auxin transport and signalling across only a few cell layers. In addition, photoreceptors can directly interact with components in the auxin signalling pathway, such as Auxin/Indole Acetic Acids (AUX/IAAs) and ARFs. Here we will discuss the complex interactions between photoreceptor and auxin signalling, addressing both mechanisms and consequences of these highly interconnected pathways.

Shade avoidance responses become more aggressive in warm environments

When exposed to neighbour cues, competitive plants increase stem growth to reduce the degree of current or future shade. The aim of this work is to investigate the impact of weather conditions on the magnitude of shade avoidance responses in Arabidopsis thaliana. We first generated a growth rate database under controlled conditions and elaborated a model that predicts daytime hypocotyl growth as a function of the activity of the main photosensory receptors (phytochromes A and B, cryptochromes 1 and 2) in combination with light and temperature inputs. We then incorporated the action of thermal amplitude to account for its effect on selected genotypes, which correlates with the dynamics of the growth-promoting transcription factor PHYTOCHROME-INTERACTING FACTOR 4. The model predicted growth rate in the field with reasonable accuracy. Thus, we used the model in combination with a worldwide data set of current and future whether conditions. The analysis predicted enhanced shade avoidance responses as a result of higher temperatures due to the geographical location or global warming. Irradiance and thermal amplitude had no effects. These trends were also observed for our local growth rate measurements. We conclude that, if water and nutrients do not become limiting, warm environments enhance the shade avoidance response.

COP1 destabilizes DELLA proteins in Arabidopsis

DELLA transcriptional regulators are central components in the control of plant growth responses to the environment. This control is considered to be mediated by changes in the metabolism of the hormones gibberellins (GAs), which promote the degradation of DELLAs. However, here we show that warm temperature or shade reduced the stability of a GA-insensitive DELLA allele in Arabidopsis thaliana Furthermore, the degradation of DELLA induced by the warmth preceded changes in GA levels and depended on the E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1). COP1 enhanced the degradation of normal and GA-insensitive DELLA alleles when coexpressed in Nicotiana benthamiana. DELLA proteins physically interacted with COP1 in yeast, mammalian, and plant cells. This interaction was enhanced by the COP1 complex partner SUPRESSOR OF phyA-105 1 (SPA1). The level of ubiquitination of DELLA was enhanced by COP1 and COP1 ubiquitinated DELLA proteins in vitro. We propose that DELLAs are destabilized not only by the canonical GA-dependent pathway but also by COP1 and that this control is relevant for growth responses to shade and warm temperature.

MYCs and PIFs Act Independently in Arabidopsis Growth Regulation

Plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light, collectively called the shade avoidance syndrome (SAS). Plants also have extensive systems to defend themselves against pathogens and herbivores. Defense and shade avoidance are two fundamental components of plant survival and productivity, and there are often tradeoffs between growth and defense. Recently, MYC2, a major positive regulator of defense, was reported to inhibit elongation during shade avoidance. Here, we further investigate the role of MYC2 and the related MYC3 and MYC4 in shade avoidance, and we examine the relationship between MYC2/3/4 and the PIF family of light-regulated transcription factors. We demonstrate that MYC2/3/4 inhibit both elongation and flowering. Furthermore, using both genetic and transcriptomic analysis we find that MYCs and PIFs generally function independently in growth regulation. However, surprisingly, the pif4/5/7 triple mutant restored the petiole shade avoidance response of myc2 (jin1-2) and myc2/3/4 We theorize that increased petiole elongation in myc2/3/4 could be more due to resource tradeoffs or post-translational modifications rather than interactions with PIF4/5/7 affecting gene regulation.

[BBX transcriptional factors family in plants-a review]

Transcriptional factors play important roles in plant growth, development and responses to stresses. BBX transcriptional factors are characterized with one or two B-box domains in the protein sequence. They are comprehensively involved in photomorphogenesis, flowering, shade avoidance, signal transduction of phytohormones, biotic and abiotic stress responses in plants by regulating gene transcription and interacting with other transcription factors. The classification, structure and functions of BBX of plants are reviewed in this paper.

Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B

The constitutively active missense allele of Arabidopsis phytochrome B, AtPHYBY276H or AtYHB, encodes a polypeptide that adopts a light-insensitive, physiologically active conformation capable of sustaining photomorphogenesis in darkness. Here, we show that the orthologous OsYHB allele of rice phytochrome B (OsPHYBY283H ) also encodes a dominant "constitutively active" photoreceptor through comparative phenotypic analyses of AtYHB and OsYHB transgenic lines of four eudicot species, Arabidopsis thaliana, Nicotiana tabacum (tobacco), Nicotiana sylvestris and Solanum lycopersicum cv. MicroTom (tomato), and of two monocot species, Oryza sativa ssp. japonica and Brachypodium distachyon. Reciprocal transformation experiments show that the gain-of-function constitutive photomorphogenic (cop) phenotypes by YHB expression are stronger in host plants within the same class than across classes. Our studies also reveal additional YHB-dependent traits in adult plants, which include extreme shade tolerance, both early and late flowering behaviors, delayed leaf senescence, reduced tillering, and even viviparous seed germination. However, the strength of these gain-of-function phenotypes depends on the specific combination of YHB allele and species/cultivar transformed. Flowering and tillering of OsYHB- and OsPHYB-expressing lines of rice Nipponbare and Kitaake cultivars were compared, also revealing differences in YHB/PHYB allele versus genotype interaction on the phenotypic behavior of the two rice cultivars. In view of recent evidence that the regulatory activity of AtYHB is not only light insensitive but also temperature insensitive, selective YHB expression is expected to yield improved agronomic performance of both dicot and monocot crop plant species not possible with wild-type PHYB alleles.

Phytochrome evolution in 3D: deletion, duplication, and diversification

Canonical plant phytochromes are master regulators of photomorphogenesis and the shade avoidance response. They are also part of a widespread superfamily of photoreceptors with diverse spectral and biochemical properties. Plant phytochromes belong to a clade including other phytochromes from glaucophyte, prasinophyte, and streptophyte algae (all members of the Archaeplastida) and those from cryptophyte algae. This is consistent with recent analyses supporting the existence of an AC (Archaeplastida + Cryptista) clade. AC phytochromes have been proposed to arise from ancestral cyanobacterial genes via endosymbiotic gene transfer (EGT), but most recent studies instead support multiple horizontal gene transfer (HGT) events to generate extant eukaryotic phytochromes. In principle, this scenario would be compared to the emerging understanding of early events in eukaryotic evolution to generate a coherent picture. Unfortunately, there is currently a major discrepancy between the evolution of phytochromes and the evolution of eukaryotes; phytochrome evolution is thus not a solved problem. We therefore examine phytochrome evolution in a broader context. Within this context, we can identify three important themes in phytochrome evolution: deletion, duplication, and diversification. These themes drive phytochrome evolution as organisms evolve in response to environmental challenges.

Competition at the soybean V6 stage affects root morphology and biochemical composition

The experiment was conducted in the 2016/17 crop season in a greenhouse at Passo Fundo University, Brazil. We hypothesised that the morphological characteristics and biochemical and anatomical composition of soybean roots and shoots, when competing with weeds during different growth periods, are negatively affected, so current concepts of competition between plants should also consider changes in plant roots. The soybean cultivar P 95R51 and horseweed (Conyza bonariensis) were used. The treatments consisted of the presence or absence of weeds during different coexistence periods of soybean with horseweed. The periods were V0-V3, V0-V6, V0-R2, V3-R6, V6-R6 and R2-R6, where V0 was the date of soybean sowing and V3, V6, R2 and R6 were phenological stages of the crop. Two fresh roots were used to examine morphological traits. Four roots were used for quantification of dry matter and secondary metabolites. Root length was reduced by 21%, 14% and 20% when competing with a weed in the V0-V3, V0-V6 and R2-R6 coexistence periods, respectively. Total phenol content in the V0-V6 and V0-R2 periods was reduced when plants were in competition with weeds; a similar trend was found for flavonoids in the V0-V6 period. Soybean-horseweed competition from crop emergence to the V6 stage, in general, affects shoot and root morphological traits and the biochemical composition of the soybean roots. The presence of horseweed at the V3, V6 and R2 stages does not negatively alter the traits evaluated. Root anatomical composition is not modified during all coexistence periods with horseweed.

Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PIF proteins

Light-environment signals, sensed by plant phytochrome photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown "trans factors" modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of colocalization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator to regulate the expression of PIF-DTGs through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF-signaling hub.

HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion

Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the YUCCA8 locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with YUCCA8, allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.

Effects of Continuous or End-of-Day Far-Red Light on Tomato Plant Growth, Morphology, Light Absorption, and Fruit Production

Shading by sunlit leaves causes a low red (R) to far-red (FR) ratio that results in a low phytochrome stationary state (PSS). A low PSS induces an array of shade avoidance responses that influence plant architecture and development. It has often been suggested that this architectural response is advantageous for plant growth due to its positive effect on light interception. In contrast to sunlight, artificial light sources such as LEDs often lack FR, resulting in a PSS value higher than solar light (∼0.70). The aim of this study was to investigate how PSS values higher than solar radiation influence the growth and development of tomato plants. Additionally, we investigated whether a short period of FR at the end of the day (EOD-FR) could counteract any potentially negative effects caused by a lack of FR during the day. Tomato plants were grown at four PSS levels (0.70, 0.73, 0.80, and 0.88), or with a 15-min end-of-day far-red (EOD-FR) application (PSS 0.10). Photosynthetic Active Radiation (PAR; 150 μmol m-2 s-1) was supplied using red and blue (95/5%) LEDs. In an additional experiment, the same treatments were applied to plants receiving supplementary low-intensity solar light. Increasing PSS above solar PSS resulted in increased plant height. Leaf area and plant dry mass were lower in the treatments completely lacking FR than treatments with FR. EOD-FR-treated plants responded almost similarly to plants grown without FR, except for plant height, which was increased. Simulations with a 3D-model for light absorption revealed that the increase in dry mass was mainly related to an increase in light absorption due to a higher total leaf area. Increased petiole angle and internode length had a negative influence on total light absorption. Additionally, the treatments without FR and the EOD-FR showed strongly reduced fruit production due to reduced fruit growth associated with reduced source strength and delayed flowering. We conclude that growing tomato plants under artificial light without FR during the light period causes a range of inverse shade avoidance responses, which result in reduced plant source strength and reduced fruit production, which cannot be compensated by a simple EOD-FR treatment.

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.

Quantitative proteomic analyses identified multiple sugar metabolic proteins in soybean under shade stress

Soybean-based intercropping is important for sustainable agricultural practice on a regional and global scale. However, most soybean varieties use shade avoidance strategy to acquire more light absorption when suffered in canopy shade in intercropping systems, thus reduced the yield of the whole population on a farmland. The mechanisms underlying early response of soybean in shade avoidance is still largely unknown. Here we report our identification of differentially accumulated proteins in shade-sensitive soybean seedlings by global quantitative proteome analysis under white light (WL) and shade conditions. By using Tandem Mass Tag (TMT) labelling and HPLC fractionation followed by high-resolution LC-MS/MS analysis, 29 proteins were found up-regulated and 412 proteins were found down-regulated in soybean seedlings by 2-h shade stress than that by 2-h WL treatment. Multiple differentially expressed proteins are enriched in carbohydrate metabolic process especially in the biosynthetic pathways of cell wall polysaccharides in soybean seedlings by shade stress comparing to those in WL growth conditions. Physiological assays showed that saccharides were rapidly declined in shoot apex of soybean seedlings under a short-term shading. Our results would provide new insights into the mechanisms of shade avoidance responses in soybean seedlings.

Ecological significance of light quality in optimizing plant defence

Plants balance the allocation of resources between growth and defence to optimize fitness in a competitive environment. Perception of neighbour-detection cues, such as a low ratio of red to far-red (R:FR) radiation, activates a suite of shade-avoidance responses that include stem elongation and upward leaf movement, whilst simultaneously downregulating defence. This downregulation is hypothesized to benefit the plant either by mediating the growth-defence balance in favour of growth in high plant densities or, alternatively, by mediating defence of individual leaves such that those most photosynthetically productive are best protected. To test these hypotheses, we used a 3D functional-structural plant model of Brassica nigra that mechanistically simulates the interactions between plant architecture, herbivory, and the light environment. Our results show that plant-level defence expression is a strong determinant of plant fitness and that leaf-level defence mediation by R:FR can provide a fitness benefit in high densities. However, optimal plant-level defence expression does not decrease monotonically with plant density, indicating that R:FR mediation of defence alone is not enough to optimize defence between densities. Therefore, assessing the ecological significance of R:FR-mediated defence is paramount to better understand the evolution of this physiological linkage and its implications for crop breeding.