Biology subjects

Pierik, R.

Publications and source records attributed to Pierik, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Shoot to root transport of the HY5 transcription factor drives root developmental plasticity under neighbour shade.

Plants perceive competitors through the reflection of Far-Red light from neighbouring leaves. A decrease in the Red: Far-red light ratio (R:FR) is perceived by phytochrome photoreceptors and triggers elongation responses aboveground, allowing plants to anticipate future competition for light; their primary energy source. However, low R:FR perception by the shoot also prompts an alteration of root development, possibly to conserve resources. An important regulator of this response is the bZIP transcription factor ELONGATED HYPOCOTYL 5 (HY5), which can be transported from the shoot to the root, where it suppresses auxin signaling and lateral root outgrowth. However, it remains unknown whether HY5 transport is the direct link between shoot-perceived low R:FR and a decrease in lateral root outgrowth. We therefore sought to uncover the mechanics and speed of HY5 transport. To this end, we constructed shoot-specific inducible lines to perform live-imaging of HY5 transport using a vertical confocal microscope. This allowed us to follow the transport and unloading of HY5 from the phloem into the protophloem pericycle, where it becomes nuclearly localized, in real time over a 24-hour period. To mimic plant competition, we applied supplemental FR light and observed that this increased the HY5 protein levels in the shoot and subsequent HY5 protein transport from shoot-to-root. Finally, we were able to show that shoot-expressed HY5 is necessary and sufficient to induce the root response to shoot perceived Far-Red light. This work showcases in detail how a small general transcription factor functions as a long-distance signal between shoot and root and integrates environmental signalling over long distances in the plant.

plant biology↗

bioRxiv2026

Local and distal signals drive cell-type-specific leaf responses during shade avoidance

Plants reposition and grow their leaves towards optimal light conditions in a canopy. To achieve both horizontal and vertical displacement, plants need to simultaneously elongate their cells unidirectionally and maintain an elongation rate differential between the abaxial and adaxial side of the organ to bend. Exposure to Far-Red (FR) light enrichment can induce both responses, depending on where FR is sensed. Here we studied how plants maintain both growth responses simultaneously within the same organ. To deduce the regulatory mechanisms governing the simultaneous regulation of differential and unidirectional elongation, we performed both organ specific and single cell RNA sequencing experiments on plants exposed to local or whole plant FR enrichment. Single cell transcriptomics resolved that FR light signalling occurs through all cell types, but core components of the shade avoidance pathway are expressed cell type-specifically and require signalling across tissues to control growth plasticity. The upstream photoreceptor targets, including auxin biosynthesis-associated genes, in the leaf lamina are expressed in the epidermis, whilst auxin response gene expression in the petiole occurs also in the deeper tissues layers. We thus identified the remotely triggered differential growth transcriptome acting in the abaxial cortex and show that this is complemented by locally induced second transcriptome signature that is associated with unidirectional petiole elongation. The latter is induced across all cell types. We propose that this spatial distinction of transcriptional regulation of gene clusters could represent how differential and unidirectional growth can occur simultaneously in the same organ under FR light enrichment.

plant biology↗

bioRxiv2025

PlantCV v4: Image analysis software for high-throughput plant phenotyping

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. CORE IDEASO_LIPlantCV is an open-source, open-development, Python-based software package that has a new release for improved functionality and usability to make image analysis flexible and easier for researchers without a coding background. C_LIO_LIPlantCV is now capable of handling new data types that are relevant to researchers, such as thermal and hyperspectral, and has built in functionality for extracting information from these image types. C_LIO_LIThe software project aims to lower the barrier to entry into image analysis for researchers by providing numerous, versioned, interactive tutorials that cover most common use cases, particularly in plant science. C_LI

plant biology↗

bioRxiv2025

The Lettuce Expression Browser: from lab to LEB

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. Significance statementThe Lettuce Expression Browser (LEB) provides the first high-resolution gene expression atlas for both cultivated and wild lettuce species. This open-access resource enables detailed exploration of gene activity across development stages and stress conditions, advancing functional genomics in the Asteraceae family.

plant biology↗

bioRxiv2024

Pith cell responses to low red: far-red light in dicot stems

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.

plant biology↗

bioRxiv2024

Ensuring Robustness in Scientific Research, Split-root assays as an example case

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 results and provide concrete recommendations for enhancing replicability and robustness of these and other complex experiments through extending the level of detail in research protocols.

plant biology↗

bioRxiv2024

Brassinosteroid and gibberellin signaling are required for Tomato internode elongation in response to low red: far-red light

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 hormones 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. HighlightThis study unveils the interplay of brassinosteroids and gibberellins in shade avoidance elongation, revealing how tomatoes acclimate in response to far-red enriched light conditions.

plant biology↗

bioRxiv2023

Phytochrome-dependent responsiveness to root-derived cytokinins enables coordinated elongation responses to combined light and nitrate cues.

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 used a combination of transcriptomics, growth assays and dedicated genetic and pharmacological interventions to demonstrate how Arabidopsis integrates light and nitrate signalling. We unveiled that nitrate modulates shade avoidance via a previously unknown shade response pathway that involves root-derived transZeatin (tZ). 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.

plant biology↗

bioRxiv2023

Shoot-to-root mobile CEPD proteins regulate TGA transcription factors to allow nitrate root-to-shoot transport in Arabidopsis thaliana

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.

plant biology↗

bioRxiv2023

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

Plant organs move throughout the diurnal cycle, changing leaf and petiole positions to balance light capture, leaf temperature and water loss under dynamic environmental conditions. Upward movement of the petiole, called hyponasty, is one of several traits of the shade avoidance syndrome (SAS). SAS traits are elicited upon perception of vegetation shade signals such as far-red light (FR) and improve light capture in dense vegetation. Monitoring plant movement at a high temporal resolution allows studying functionality, as well as 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 set-up, based on small Raspberry Pi computers, that can track leaf movements and elongation growth with high temporal resolution. We also developed an open-source, semi-automated image analysis pipeline. Using this setup we followed responses to FR enrichment, light intensity and their interactions. Tracking both elongation and angle of petiole, lamina and entire leaf revealed insight into R:FR sensitivities of leaf growth and movement dynamics, and its interactions with background light intensity. We also identified spatial separation in hyponastic response regulation for the petiole and the lamina of the leaf, depending on the light conditions.

plant biology↗

bioRxiv2023

Gibberellin transport affects (lateral) root growth through HY5 during Far-Red light enrichment.

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.

plant biology↗

bioRxiv2022

Local light signalling 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 neighbours 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 light signalling promotes auxin accumulation in the abaxial petiole by reinforcing an intrinsic auxin transport directionality. In the petiole, auxin elicits a response of both auxin 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 results reveal how plants can spatially relay information about neighbour proximity from their sensory leaf tips to the petiole base, thus driving adaptive growth.

plant biology↗

bioRxiv2022

Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics

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

plant biology↗

bioRxiv2021

Towards increased shading potential: a combined phenotypic and genetic analysis of rice shoot architecture

Rice feeds more than half of the worlds human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice diversity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the diversity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plants ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated diversity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture. One sentence summaryThrough screening a rice diversity panel for variation in shoot architecture, we identified traits corresponding to plant shading potential and their genetic constituents.

plant biology↗

bioRxiv2021

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 suppressed. 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.

plant biology↗

bioRxiv2021

Mechanisms of far-red light-mediated dampening of defense against Botrytis cinerea in tomato leaves

Plants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth-defense trade-off. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungus Botrytis cinerea (B.c.). We monitored the leaf transcriptional changes over a 30-hr time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general dampening of B.c.-responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affect plant immune responses under WL+FR conditions. This study increases our understanding of the growth-immunity trade-off, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems. One-sentence summaryLow Red:Far-red ratio enhances tomato susceptibility towards the necrotrophic fungus Botrytis cinerea via delayed early pathogen detection and dampening of jasmonic acid-mediated defense activation.

plant biology↗

bioRxiv2020

Far-red light enhances soluble sugar levels and Botrytis cinerea disease development in tomato leaves in a jasmonate-dependent manner

Plants lacking phytochrome photoreceptors display elevated soluble sugar levels in leaves. Although pathogens principally feed on sugars supplied by the plant, the link between increased plant sugar levels upon phytochrome inactivation and disease development has not been considered. Tomato plants were exposed to control white LED (WL) or a combination of white and far-red LED (WL+FR) light, to inactivate phytochrome signaling and modulate soluble sugar levels. We also experimentally manipulated internal sugar levels by either supplementing glucose or inhibiting photosynthesis in tomato leaflets prior to performing soluble sugar quantifications or bioassays with pathogens. Tomato plants exposed to WL+FR or lacking phytochrome B (phyB1phyB2 double mutants) show enhanced levels of soluble sugars, especially glucose and fructose, in their leaves. The jasmonic acid biosynthesis mutant def1 also has elevated soluble sugar levels, which could be rescued by exogenous methyl-jasmonate application. This indicates an interplay between JA signaling and primary metabolism. The increase in soluble sugar levels in tomato leaves upon phytochrome inactivation is regulated in a JA-dependent manner. Our data stress the importance of primary metabolism in the FR-induced susceptibility in tomato that could contribute to promote plant resistance when grown at high density.

plant biology↗

bioRxiv2020

A gas-and-brake mechanism of bHLH proteins modulates shade avoidance in Arabidopsis thaliana

Plants detect proximity of competitors through reduction in the ratio between red and far red light triggering the shade avoidance syndrome, which includes accelerated shoot elongation and early flowering. Shade avoidance is regulated through PHYTOCHROME INTERACTING FACTORs (PIFs), a group of bHLH transcription factors. Another (b)HLH protein, KIDARI (KDR), which is non-DNA-binding, was identified in de-etiolation studies and proposed to interact with LONG HYPOCOTYL IN FAR-RED 1 (HFR1), a (b)HLH protein that inhibits shade avoidance. Here we establish novel roles of KDR in regulating shade avoidance and investigate how KDR regulates the shade avoidance network. We show that KDR is a positive regulator of shade avoidance and interacts with several negative growth regulators. We identify novel interactors using a combination of yeast two-hybrid screening and dedicated confirmations with bimolecular fluorescence complementation. We demonstrate that KDR is translocated primarily to the nucleus when coexpressed with these newly discovered interactors. A genetic approach confirmed that several of these novel interactions are indeed functional to shade avoidance in Arabidopsis thaliana, whereas we propose that KDR does not interact with HFR1 to regulate shade avoidance. Based on this, we propose that shade avoidance is regulated by a three-layered gas-and-brake mechanism of bHLH protein interactions, adding an additional layer of complexity to what was previously known. One-sentence summaryKIDARI is a positive regulator of shade avoidance and part of a three-layer network of bHLH transcription factor interactions.

plant biology↗