Responses to far-red light are mediated by phytochromes, specialized photoreceptors present in all organs of a tomato plant (Solanum lycopersicum L.). Although fruit-localized phytochromes can influence starch and sugar metabolism, their involvement in modulating fruit growth responses to far-red light is unknown. We explored whether fruit growth responses to far-red light are driven by local far-red perception within the fruits or by a systemic response initiated in the vegetative organs. We applied far-red light exclusively to the fruiting trusses, to the vegetative organs, to both, or to neither. Far-red light was added to a constant red-white LED background spectrum to simulate greenhouse supplementary lighting. We quantified plant and fruit growth responses to far-red and performed a transcriptomic analysis to establish the temporal dynamics of far-red light perception and signaling in leaves and fruits. Supplementing far-red light to the vegetative organs increased ripe fruit weight and sugar concentration, whereas far-red supplementation to the generative organs alone had no measurable effect. This study establishes that far-red perception by vegetative organs drives fruit growth responses in tomato. Local responses to far-red light included a transient increase in auxin concentration and upregulation of the auxin-signaling pathway in leaves, a conserved response to decreasing red/far-red ratios. In fruits, early transcriptomic responses carried signatures of auxin, cytokinin, and gibberellin biosynthesis and signaling, suggesting a role for hormones as mediators of far-red-induced fruit responses. This work reveals how responses to far-red light perception by vegetative organs promote sink strength and starch biosynthesis in early developing fruits, contributing to higher fruit weight and sugar concentration in ripe fruits.

Plants use light both as a resource for photosynthesis and as a signal about their environment. In response to light cues, plants can move their organs via directional growth driven by cell expansion. In dense vegetation where light is available in spatially heterogeneous patterns, plants need to navigate this space to improve the position of their photosynthetic tissues. In canopies blue light irradiance and red to far-red light ratio decrease due to absorption by chloroplasts, and these changes regulate distinct processes within the plant. Changes in light environment are detected by cryptochrome and phytochrome photoreceptors, both regulating phytochrome interacting factors (PIFs) and thereby enhancing elongation in hypocotyls, stems, and leaves and inducing upward leaf movement (hyponasty). An additional class of photoreceptors, phototropins, decodes horizontal light gradients to produce directional growth toward the light source (phototropism). Here we review the current state of knowledge on these differential growth responses to light cues, with specific emphasis on the regulatory pathways that translate light signaling into differential cell expansion. Downstream of the photoreceptors, the phytohormone auxin induces cell growth in shoot tissues, but also other phytohormones contribute to balancing light responses. Cell expansion is regulated primarily at the level of cell walls, and a comparison of different transcriptome datasets reveals that only a small group of cell wall-modifying genes are tightly regulated by shade cues. It remains poorly understood which cell layers are causal to the initiation of cellular expansion. Here we combine insights from different differential growth behaviors in different species and organs to generate different hypotheses for the cellular underpinnings of light-driven leaf movements.

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data, and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection.

Lettuce (Lactuca sativa L.) is an economically important leafy vegetable within the Asteraceae family, cultivated worldwide across diverse agricultural systems. Recent advances in genomic and transcriptomic resources have positioned lettuce as a promising model system for functional genomics in the Asteraceae. However, currently available gene expression datasets lack comprehensive tissue-specific resolution, primarily focus on a single cultivar and are not visualised in an interpretable manner, limiting their utility for broader genetic and physiological studies. To bridge this gap, we developed the Lettuce Expression Browser (LEB), a publicly available platform providing high-resolution gene expression maps across various organs, tissues and developmental stages in both cultivated and wild lettuce species. The LEB integrates transcriptomic data from finely dissected seedlings, shoot tissues at various developmental stages and seedlings subjected to abiotic stresses (salt and far-red), visualised using the ggPlantmap R package. This platform offers an intuitive interface for exploring gene expression patterns and serves as a valuable resource for those studying lettuce development, stress responses and evolutionary genomics. The LEB is hosted on the LettuceKnow Web Portal (https://lettuce.bioinformatics.nl) and can be expanded to include additional datasets, enhancing its role as a key tool for lettuce research and crop improvement.

Potassium ion (K + ) is essential for plant growth and development. Despite decades of study, the Shaker -type K + channel AKT5 has remained functionally unassigned. Here, we report that AKT5 functions as a bona fide voltage-dependent K + channel and serves as an essential regulator of petiole elongation. Structural analyses of AKT5 in a closed state and the AKT5-D403 variant in a pre-open state provide direct structural evidence for functional K + channel activity. AKT5 assembled into a canonical tetramer with two-fold symmetry and, upon phosphorylation, operated as an inward-rectifying K + channel activated at strongly hyperpolarized membrane potentials. AKT5 was predominantly expressed in young petioles, and loss of AKT5 function largely suppressed petiole elongation throughout the diurnal cycle, resulting in compact rosettes and reduced biomass under crowded growth conditions. These findings show that AKT5 is involved in a regulator of plant competitive growth and high-density performance.

Plants compete for light by growing taller than their nearest competitors. This is part of the shade avoidance syndrome and is a response to an increase in far-red (FR) light reflected from neighboring leaves. The root responds to this shoot-sensed FR cue by reducing lateral root emergence. It is well established that the phytohormone gibberellic acid (GA) is involved in supplemental FR-induced shoot elongation. Although GA is transported from shoot to root, its role in regulating lateral root growth is unclear. Here, we chemically and genetically manipulated GA and showed that GA modulates the lateral root reduction induced by shoot-sensed FR enrichment in Arabidopsis (Arabidopsis thaliana). Using the FRET-based GA biosensor GPS1 (GIBBERELLIN PERCEPTION SENSOR 1), we observed detailed GA changes in the root upon shoot exposure to FR enrichment and upon GA application to the shoot. Supplying GA to the shoot mitigated the FR-enrichment-induced root phenotype, indicating a functional link between GA and changes in root development in response to shoot-sensed FR. The regulatory role of GA in root growth appears to be partially dependent on ELONGATED HYPOCOTYL 5 (HY5), a light-responsive transcription factor that regulates root growth. Shoot-to-root transported GA4 led to increased HY5 protein levels in the lateral root primordia. HY5 then repressed auxin signaling, which inhibited lateral root growth. Our data reveal a gibberellin-dependent mechanism through which above-ground FR light signals modulate lateral root growth, whereby phytohormone and light signaling coordinate development across spatial scales.

Scientific progress relies on reproducibility, replicability, and robustness of research outcomes. After briefly discussing these terms and their significance for reliable scientific discovery, we argue for the importance of investigating robustness of outcomes to experimental protocol variations. We highlight challenges in achieving robust, replicable results in multi-step plant science experiments, using split-root assays in Arabidopsis thaliana as a case study. These experiments are important for unraveling the contributions of local, systemic and long-distance signalling in plant responses and play a central role in nutrient foraging research. The complexity of these experiments allows for extensive variation in protocols. We investigate what variations do or do not result in similar outcomes and provide concrete recommendations for enhancing the replicability and robustness of these and other complex experiments by extending the level of detail in research protocols.

In dense canopies, light becomes a limiting factor for plant growth. Many plants respond to neighbor cues by growing taller to improve light capture, a phenomenon known as the shade avoidance syndrome (SAS). The major neighbor detection is via enrichment of far-red (FR) light that leads to a low red:far-red light ratio (R:FR), suppressing phytochrome activity. In tomato, low R:FR induces elongation of the internodes, but study into the role of different cell types in this response has remained limited. We characterized changes in cellular anatomy of the tomato internode in response to low R:FR and its accompanying changes in gene expression. We observed changes to the pith traits, including increases in pith layer number, pith cell diameter, and longitudinal cell length. We profiled the transcriptome in the entire internodes and in the hand-dissected pith in the central cylinder of the internode in response to low R:FR treatment and identified transcription factors (TFs) of interest that were upregulated in the central cylinder, mostly GATA, TCP, and bZIPs. We then characterized FR responses in eight dicotyledonous species. Significant pith elongation was observed in species that exhibited a strong internode elongation response. The FR-responsive expression of homologs of target GATA, TCP, and bZIP TFs in the central cylinder was conserved within the Solanaceae family. Overall, we discovered central cylinder gene expression patterns in SAS that are distinct from those of the entire internode, suggesting that some responses are unique and likely specific to vascular cell types such as pith. These patterns were conserved with close relatives of tomato but not in other dicot families we sampled, indicating that different molecular mechanisms drive FR responses in different dicots.

Plants growing in dense vegetation 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. Below ground, root development is also adjusted in response to above-ground neighbour proximity. Canopies are dynamic and complex environments with heterogeneous light cues in the far-red, red, blue, and UV spectrum, which can be perceived by photoreceptors in spatially separated plant tissues. Molecular regulation of plant architecture adjustment via PHYTOCHROME-INTERACTING FACTOR 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 review recent advances in how plants respond to heterogeneous light cues and integrate these with other environmental signals.

Leaf photosynthesis models are used extensively in photosynthesis research and are embedded in many larger scale models. Typical photosynthesis models simplify light intensity as the integrated intensity over the 400-700 nm waveband (photosynthetic active radiation, PAR). However, far-red light (700-750 nm, FR) also drives photosynthesis when supplied in addition to light within the PAR spectrum. Currently, it is unknown how much far-red light contributes to carbon assimilation under various spectral light conditions. We developed a combined experimental and computational method to quantify FR stimulation. Gas-exchange parameters and incident light spectra were measured simultaneously and analysed with wavelength-dependent modelling of light harvesting. Hereto, separate excitation of Photosystem I and Photosystem II was calculated from incident light spectra. The effect of FR supplementation on photosynthesis was subsequently modelled and expressed as a single parameter ρ. We tested our method on Solanum dulcamara, Lactuca sativa and Phaseolus vulgaris under various light conditions. Results show consistent ρ-values across a range of FR levels. Our method provides an approach to consistently quantify the effect of FR stimulation on photosynthesis and harmonise the interpretation of photosynthesis measurements under different light regimes, for example in (experimental) setups with artificial FR supplementation or in canopies.

In this study, we explore the interplay between the plant hormones gibberellins (GA), brassinosteroids (BR), and Indole-3-Acetic Acid (IAA) in their collective impact on plant shade avoidance elongation under varying light conditions. We focus particularly on low Red:Far-red (R:FR) light conditions achieved by supplementing the background light with FR. We characterized the tomato internode response to low R:FR and, with RNA-seq analysis, we were able to identify some of the potential regulatory hormonal pathways. Through a series of exogenous pharmacological modulations of GA, IAA, and BR, we demonstrate that GA and BR are sufficient but also necessary for inducing stem elongation under low R:FR light conditions. Intriguingly, while IAA alone shows limited effects, its combination with GA yields significant elongation, suggesting a nuanced hormonal balance. Furthermore, we unveil the complex interplay of these hormones under light with low R:FR, where the suppression of one hormone's effect can be compensated by the others. This study provides insights into the hormonal mechanisms governing plant adaptation to light, highlighting the intricate and adaptable nature of plant growth responses. Our findings have far-reaching implications for agricultural practices, offering potential strategies for optimizing plant growth and productivity in various lighting environments.

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.

In this study, we explore the dynamic interplay between the plant hormones gibberellins (GA), brassinosteroids (BR), and Indole-3-Acetic Acid (IAA) in their collective impact on plant shade avoidance elongation under varying light conditions. We focus particularly on low Red: Far-red (R:FR) light conditions achieved by supplementing the background light with FR. Our research delves into how these hormones individually and synergistically influence stem elongation in tomato plants. Through meticulous experimental modulations of GA, IAA, and BR, we demonstrate that GA and BR are sufficient but also necessary for inducing stem elongation under low R:FR light conditions. Intriguingly, while IAA alone shows limited effects, its combination with GA yields significant elongation, suggesting a nuanced hormonal balance. Furthermore, we unveil the complex interplay of these hormones under light with low R:FR, where the suppression of one hormone’s effect can be compensated by the others. This study provides insights into the hormonal mechanisms governing plant adaptation to light, highlighting the intricate and adaptable nature of plant growth responses. Our findings have far-reaching implications for agricultural practices, offering potential strategies for optimizing plant growth and productivity in various lighting environments.Highlight This study unveils the interplay of brassinosteroids and gibberellins in shade avoidance elongation, revealing how tomatoes acclimate in response to far-red enriched light conditions.### Competing Interest StatementThe authors have declared no competing interest.* SAS : Shade avoidance syndrome GA : Gibberellins BR : Brassinosteroids IAA : Indole-3-Acetic Acid R : red light FR : Far-red light WL : White light DEG : Differentially expressed genes GO : Gene Ontology NPA : Naphthylphthalamic acid BBo : 4-biphenylboronic acid PEO-IAA : 2-(1H-Indol-3-yl)-4-oxo-4-phenyl-butyric acid PBZ : Paclobutrazol BZ : Brassinazole

In dense canopies light becomes a limiting factor for plant growth. Many plants respond to neighbor cues by growing taller to improve light capture, a phenomenon known as the shade avoidance syndrome (SAS). The major neighbor detection is via enrichment of far-red (FR) light that leads to a low red: far-red light ratio (R:FR), suppressing phytochrome activity. In tomato, low R:FR induces elongation of the internodes, but study into the role of different cell types in this response has remained limited. We characterized changes in cellular anatomy of the tomato internode in response to low R:FR, and its accompanying changes in gene expression. We observed changes to the pith traits, including increases in pith layer number, pith cell diameter and longitudinal cell length. We profiled the transcriptome in the entire internodes and in the hand-dissected pith in the central cylinder of the internode in response to low R:FR treatment and identified transcription factors (TFs) of interest that were upregulated in the central cylinder, mostly GATA, TCP, and bZIPs. We then characterized FR-responses in eight dicotyledonous species. Significant pith elongation was observed in species that exhibited a strong internode elongation response. The FR-responsive expression of homologs of target GATA, TCP and bZIP TFs in the central cylinder was conserved within the Solanaceae family. Overall, we discovered central cylinder gene expression patterns in SAS that are distinct from those of the entire internode, suggesting that some responses are unique and likely specific to vascular cell types such as pith. These patterns were conserved with close relatives of tomato but not in other dicot families we sampled, indicating that different molecular mechanisms drive FR responses in different dicots. ### Competing Interest Statement The authors have declared no competing interest.

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

Plants growing at high densities can detect competitors through changes in the composition of light reflected by neighbours. In response to this far-red-enriched light, plants elicit adaptive shade avoidance responses for light capture, but these need to be balanced against other input signals, such as nutrient availability. Here, we investigated how Arabidopsis integrates shade and nitrate signalling. We unveiled that nitrate modulates shade avoidance via a previously unknown shade response pathway that involves root-derived trans-zeatin (tZ) signal and the BEE1 transcription factor as an integrator of light and cytokinin signalling. Under nitrate-sufficient conditions, tZ promotes hypocotyl elongation specifically in the presence of supplemental far-red light. This occurs via PIF transcription factors-dependent inhibition of type-A ARRs cytokinin response inhibitors. Our data thus reveal how plants co-regulate responses to shade cues with root-derived information about nutrient availability, and how they restrict responses to this information to specific light conditions in the shoot. The authors here investigate information integration in plants using light and nutrient stimuli and identify a novel regulation pathway towards photoreceptor-regulated stem growth.

Societal Impact Statement Rice farming is transitioning from transplanting rice seedlings towards the less labour‐intensive and less water‐demanding method of directly seeding rice. This, however, is accompanied by increased weed proliferation. To tackle this issue, this study seeks to identify how the crop itself can better suppress weeds, with a focus on light competition via shading. Using a rice diversity panel, traits were identified that contribute to enhanced shading capacity, and these traits were encapsulated into a single shading capacity metric. This was followed by the identification of the genetic loci underpinning variation in the core traits. The identified haplotypes can be used in breeding programmes to improve weed suppression by rice, thus contributing to sustainable agriculture. Summary In modern rice farming, one of the major constraints is weed proliferation and the entailed ecological impact of herbicide application. This requires increased weed competitiveness in current rice varieties, achieved via enhanced shade casting to limit the growth of shade‐sensitive weeds. To identify traits that increase rice shading capacity, we exhaustively phenotyped a rice diversity panel of 344 varieties at an early vegetative stage. A genome‐wide association study (GWAS) revealed genetic loci underlying variation in canopy architecture traits linked with shading capacity. The screen shows considerable natural variation in shoot architecture for 13 examined traits, of which shading potential is mostly determined by projected shoot area, number of leaves, culm height and canopy solidity. The shading rank, a metric based on these core traits, identifies varieties with the highest shading potential. Five genetic loci were found to be associated with canopy architecture, shading potential and early vigour. Identification of traits contributing to shading capacity and underlying allelic variation will serve future genomic‐assisted breeding programmes. Implementing the presented genetic resources for increased shading and weed competitiveness in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture.

In Arabidopsis thaliana , nitrogen (N) starvation leads to increased synthesis of CEPD (C-TERMINALLY ENCODED PEPTIDE DOWNSTREAM) proteins in the shoot. CEPDs travel to the roots, where they activate expression of genes required for high affinity nitrate transport. CEPDs belong to a plant-specific class of glutaredoxin-like proteins that interact with TGACG-binding transcription factors (TGAs). Here we identified the redundant clade-I TGAs TGA1 and TGA4 as the link between CEPDs and target promoters. In the absence of CEPDs, TGA1/4 have a strong negative effect on N starvation-induced gene expression leading to reduced translocation of N from the root to the shoot and to reduced shoot fresh weight. Basal levels of CEPDs were sufficient to completely release TGA1/4-mediated repression of nitrate acquisition. The antagonism between CEPDs and TGA1/4 was also detected in shoots, where CEPDs dampened the activating function of TGA1/4 on hyponasty and defense. CEPDs encode the conserved putative active site motif CxxC/S that was suggested to mediate redox regulation of target proteins. Complementation of the tga1 tga4 mutant with a TGA1 variant containing amino acid substitutions of all four potentially redox-active cysteines showed that CEPDs do not regulate TGA1/4 by modulating their redox state.

Plants compete for light by growing taller than their nearest competitors. This is part of the shade avoidance syndrome and is a response to an increase of Far-Red light (FR) reflected from neighboring leaves. The root responds to this shoot-sensed FR cue by reducing lateral root emergence. It is well-established that the plant hormone Gibberellic Acid (GA) is involved in supplemental FR-induced shoot elongation. Although GA is also transported from shoot to root, its role in regulating lateral root growth is unclear. We show via GA manipulations, both chemical and genetic, that GA modulates the lateral root reduction induced by shoot-sensed FR enrichment. Using the FRET-based GA biosensor GPS1, we observed detailed GA changes in the root upon shoot exposure to FR enrichment and when GA was supplied to the shoot. Supplying GA to the shoot also mitigated the FR-enrichment root phenotype, indicating a functional link between GA and changes in root development in response to shoot-sensed FR. The regulatory role of GA in root growth appears to be partially dependent upon the role of ELONGATED HYPOCOTYL 5 (HY5), a light-responsive transcription factor that regulates root growth. Shoot-to-root transported GA4 led to an increase in HY5 protein levels in the lateral root primordia. HY5 then repressed auxin signaling to repress lateral root growth. Our data unveil a novel way in which hormone and light signaling coordinate development across spatial scales by adjusting (lateral) root growth from above-ground FR light signals.

A new study draws attention to photosynthetically produced sucrose as a major shoot-derived and auxin-dependent regulator of root growth and development in plants.