Phytochromes A and B mediate red-light-induced positive phototropism in roots

The Role of Light-Regulated Auxin Signaling in Root Development

The root is an important organ for obtaining nutrients and absorbing water and carbohydrates, and it depends on various endogenous and external environmental stimulations such as light, temperature, water, plant hormones, and metabolic constituents. Auxin, as an essential plant hormone, can mediate rooting under different light treatments. Therefore, this review focuses on summarizing the functions and mechanisms of light-regulated auxin signaling in root development. Some light-response components such as phytochromes (PHYs), cryptochromes (CRYs), phototropins (PHOTs), phytochrome-interacting factors (PIFs) and constitutive photo-morphorgenic 1 (COP1) regulate root development. Moreover, light mediates the primary root, lateral root, adventitious root, root hair, rhizoid, and seminal and crown root development via the auxin signaling transduction pathway. Additionally, the effect of light through the auxin signal on root negative phototropism, gravitropism, root greening and the root branching of plants is also illustrated. The review also summarizes diverse light target genes in response to auxin signaling during rooting. We conclude that the mechanism of light-mediated root development via auxin signaling is complex, and it mainly concerns in the differences in plant species, such as barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.), changes of transcript levels and endogenous IAA content. Hence, the effect of light-involved auxin signaling on root growth and development is definitely a hot issue to explore in the horticultural studies now and in the future.

Plant root growth against a mechanical obstacle: the early growth response of a maize root facing an axial resistance is consistent with the Lockhart model

Plant root growth is dramatically reduced in compacted soils, affecting the growth of the whole plant. Through a model experiment coupling force and kinematics measurements, we probed the force-growth relationship of a primary root contacting a stiff resisting obstacle, which mimics the strongest soil impedance variation encountered by a growing root. The growth of maize roots just emerging from a corseting agarose gel and contacting a force sensor (acting as an obstacle) was monitored by time-lapse imaging simultaneously to the force. The evolution of the velocity field along the root was obtained from kinematics analysis of the root texture with a particle image velocimetry derived technique. A triangular fit was introduced to retrieve the elemental elongation rate or strain rate. A parameter-free model based on the Lockhart law quantitatively predicts how the force at the obstacle modifies several features of the growth distribution (length of the growth zone, maximal elemental elongation rate and velocity) during the first 10 min. These results suggest a strong similarity of the early growth responses elicited either by a directional stress (contact) or by an isotropic perturbation (hyperosmotic bath).

Root growth direction in simulated microgravity is modulated by a light avoidance mechanism mediated by flavonols

In a microgravity environment, without any gravitropic signal, plants are not able to define and establish a longitudinal growth axis. Consequently, absorption of water and nutrients by the root and exposure of leaves to sunlight for efficient photosynthesis is hindered. In these conditions, other external cues can be explored to guide the direction of organ growth. Providing a unilateral light source can guide the shoot growth, but prolonged root exposure to light causes a stress response, affecting growth and development, and also affecting the response to other environmental factors. Here, we have investigated how the protection of the root from light exposure, while the shoot is illuminated, influences the direction of root growth in microgravity. We report that the light avoidance mechanism existing in roots guides their growth towards diminishing light and helps establish the proper longitudinal seedling axis in simulated microgravity conditions. This process is regulated by flavonols, as shown in the flavonoid-accumulating mutant transparent testa 3, which shows an increased correction of the root growth direction in microgravity, when the seedling is grown with the root protected from light. This finding may improve the efficiency of water and nutrient sourcing and photosynthesis under microgravity conditions, as they exist in space, contributing to better plant fitness and biomass production in space farming enterprises, necessary for space exploration by humans.

May the dark be with roots: a perspective on how root illumination may bias in vitro research on plant-environment interactions

Roots anchor plants to the soil, providing them with nutrients and water while creating a defence network and facilitating beneficial interactions with a multitude of living organisms and climatological conditions. To facilitate morphological and molecular studies, root research has been conducted using in vitro systems. However, under natural conditions, roots grow in the dark, mainly in the absence of illumination, except for the relatively low illumination of the upper soil surface, and this has been largely ignored. Here, we discuss the results found over the last decade on how experimental exposure of roots to light may bias root development and responses through the alteration of hormonal signalling, cytoskeleton organization, reactive oxygen species or the accumulation of flavonoids, among other factors. Illumination alters the uptake of nutrients or water, and also affects the response of the roots to abiotic stresses and root interactions with the microbiota. Furthermore, we review in vitro systems created to maintain roots in darkness, and provide a comparative analysis of root transcriptomes obtained with these devices. Finally, we identify other experimental variables that should be considered to better mimic soil conditions, whose improvement would benefit studies using in vitro cultivation or enclosed ecosystems.

A novel device to study altered gravity and light interactions in seedling tropisms

Long-duration space missions will need to rely on the use of plants in bio-regenerative life support systems (BLSSs) because these systems can produce fresh food and oxygen, reduce carbon dioxide levels, recycle metabolic waste, and purify water. In this scenario, the need for new experiments on the effects of altered gravity conditions on plant biological processes is increasing, and significant efforts should be devoted to new ideas aimed at increasing the scientific output and lowering the experimental costs. Here, we report the design of an easy-to-produce and inexpensive device conceived to analyze the effect of interaction between gravity and light on root tropisms. Each unit consisted of a polystyrene multi-slot rack with light-emitting diodes (LEDs), capable of holding Petri dishes and assembled with a particular filter-paper folding. The device was successfully used for the ROOTROPS (for root tropisms) experiment performed in the Large Diameter Centrifuge (LDC) and Random Positioning Machine (RPM) at ESA's European Space Research and Technology centre (ESTEC). During the experiments, four light treatments and six gravity conditions were factorially combined to study their effects on root orientation of Brassica oleracea seedlings. Light treatments (red, blue, and white) and a dark condition were tested under four hypergravity levels (20 g, 15 g, 10 g, 5 g), a 1 g control, and a simulated microgravity (RPM) condition. Results of validation tests showed that after 24 h, the assembled system remained unaltered, no slipping or displacement of seedlings occurred at any hypergravity treatment or on the RPM, and seedlings exhibited robust growth. Overall, the device was effective and reliable in achieving scientific goals, suggesting that it can be used for ground-based research on phototropism-gravitropism interactions. Moreover, the concepts developed can be further expanded for use in future spaceflight experiments with plants.

Spaceflight studies identify a gene encoding an intermediate filament involved in tropism pathways

We performed a series of experiments to study the interaction between phototropism and gravitropism in Arabidopsis thaliana as part of the Seedling Growth Project on the International Space Station. Red-light-based and blue-light-based phototropism were examined in microgravity and at 1g, a control that was produced by an on-board centrifuge. At the end of the experiments, seedlings were frozen and brought back to Earth for gene profiling studies via RNASeq methods. In this paper, we focus on five genes identified in these space studies by their differential expression in space: one involved in auxin transport and four others encoding genes for: a methyltransferase subunit, a transmembrane protein, a transcription factor for endodermis formation, and a cytoskeletal element (an intermediate filament protein). Time course studies using mutant strains of these five genes were performed for blue-light and red-light phototropism studies as well as for gravitropism assays on ground. Interestingly, all five of the genes had some effects on all the tropisms under the conditions studied. In addition, RT-PCR analyses examined expression of the five genes in wild-type seedlings during blue-light-based phototropism. Previous studies have supported a role of both microfilaments and microtubules in tropism pathways. However, the most interesting finding of the present space studies is that NFL, a gene encoding an intermediate filament protein, plays a role in phototropism and gravitropism, which opens the possibility that this cytoskeletal element modulates signal transduction in plants.

Conducting Plant Experiments in Space and on the Moon

The growth and development of plants during spaceflight have important implications for both basic and applied research supported by NASA and other international space agencies. While there have been many reviews of plant space biology, this chapter attempts to fill a gap in the literature on the actual process and methods of performing plant research in the spaceflight environment. One of the authors (JZK) has been a principal investigator on eight spaceflight projects. These experiences include using the U.S. Space Shuttle, the former Russian Space Station Mir, and the International Space Station, utilizing the Space Shuttle and Space X as launch vehicles. While there are several ways to fly an experiment into space and to obtain a spaceflight opportunity, this review focuses on using the NASA peer-reviewed sciences approach to get an experiment manifested for flight. Three narratives for the implementation of plant space biology experiments are considered from rapid turn around of a few months to a project with new hardware development that lasted 6 years. The many challenges of spaceflight research include logistical and resource constraints such as crew time, power, cold stowage, data downlinks, among others. Additional issues considered are working at NASA centers, hardware development, safety concerns, and the engineering versus science culture in space agencies. The difficulties of publishing the results from spaceflight research based on such factors as the lack of controls, limited sample size, and the indirect effects of the spaceflight environment also are summarized. Lessons learned from these spaceflight experiences are discussed in the context of improvements for future space-based research projects with plants. We also will consider new opportunities for Moon-based research via NASA's Artemis lunar exploration program.

PIN-mediated polar auxin transport regulations in plant tropic responses

Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underlie differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, as well as the crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

SnRK2.6 interacts with phytochrome B and plays a negative role in red light-induced stomatal opening

Light is an important environmental factor for plant growth and development. Phytochrome B (phyB), a classical red/far-red light receptor, plays vital role in controlling plant photomorphogenesis and light-induced stomatal opening. Phytohormone abscisic acid (ABA) accumulates rapidly and triggers a series of physiological and molecular events during the responses to multiple abiotic stresses. Recent studies showed that phyB mutant synthesizes more ABA and exhibits improved tolerance to salt and cold stress, suggesting that a crosstalk exists between light and ABA signaling pathway. However, whether ABA signaling components mediate responses to light remains unclear. Here, we showed that SnRK2.6 (Sucrose Nonfermenting 1-Related Protein Kinase 2.6), a key regulator in ABA signaling, interacts with phyB and participates in light-induced stomatal opening. First, we checked the interaction between phyB and SnRK2s, and found that SnRK2.2/2.3/2.6 kinases physically interacted with phyB in yeast and in vitro. We also performed co-IP assay to support that SnRK2.6 interacts with phyB in plant. To investigate the role of SnRK2.6 in red light-induced stomatal opening, we obtained the snrk2.6 mutant and overexpression lines, and found that snrk2.6 mutant exhibited a significantly larger stomatal aperture under red light treatment, while the two independent overexpression lines showed significantly smaller stomatal aperture, indicative of a negative role for SnRK2.6 in red light-induced stomatal opening. The interaction of SnRK2.6 with red light receptor and the negative role of SnRK2.6 in red light-induced stomatal opening provide new evidence for the crosstalk between ABA and red light in guard cell signaling.

Role of Light and Plant Hormones in Stem Parasitic Plant (Cuscuta and Cassytha) Twining and Haustoria Induction

Cuscuta and Cassytha are two distinct stem parasitic plant genera developing haustoria at their stem. The initial step to parasitization is twining onto the host plant. Although twining is the critical first step, less attention has been paid to this aspect in stem haustoria parasitic plant studies. As tendril coiling is also controlled by light and plant hormones, we investigated the role of light (blue, red and far-red) and hormones (auxin, brassinolide, cytokinin) in twining of stem parasitic plants (Cuscuta japonica and Cassytha filiformis). In general, both Cuscuta and Cassytha showed similar behavior to light cues. The data show that blue light is essential for twining, and a lower far-red/red light (FR/R) ratio is important for subsequent haustoria induction. Regarding plant hormones, seedlings with solely auxin or cytokinin (iP) under blue light showed not only twining but also haustoria induction, demonstrating that auxin and iP appear to be especially important for induction. Seedlings with solely brassinolide showed no positive influence, but brassinolide together with iP caused twining even under dark conditions. This points to the presence of cross-talk between brassinolide and cytokinin for twining.

From Spaceflight to Mars g-Levels: Adaptive Response of A. Thaliana Seedlings in a Reduced Gravity Environment Is Enhanced by Red-Light Photostimulation

The response of plants to the spaceflight environment and microgravity is still not well understood, although research has increased in this area. Even less is known about plants' response to partial or reduced gravity levels. In the absence of the directional cues provided by the gravity vector, the plant is especially perceptive to other cues such as light. Here, we investigate the response of Arabidopsis thaliana 6-day-old seedlings to microgravity and the Mars partial gravity level during spaceflight, as well as the effects of red-light photostimulation by determining meristematic cell growth and proliferation. These experiments involve microscopic techniques together with transcriptomic studies. We demonstrate that microgravity and partial gravity trigger differential responses. The microgravity environment activates hormonal routes responsible for proliferation/growth and upregulates plastid/mitochondrial-encoded transcripts, even in the dark. In contrast, the Mars gravity level inhibits these routes and activates responses to stress factors to restore cell growth parameters only when red photostimulation is provided. This response is accompanied by upregulation of numerous transcription factors such as the environmental acclimation-related WRKY-domain family. In the long term, these discoveries can be applied in the design of bioregenerative life support systems and space farming.

Evidence for root adaptation to a spatially discontinuous water availability in the absence of external water potential gradients

We hereby show that root systems adapt to a spatially discontinuous pattern of water availability even when the gradients of water potential across them are vanishingly small. A paper microfluidic approach allowed us to expose the entire root system of Brassica rapa plants to a square array of water sources, separated by dry areas. Gradients in the concentration of water vapor across the root system were as small as 10^-4⋅mM⋅m^-1 (∼4 orders of magnitude smaller than in conventional hydrotropism assays). Despite such minuscule gradients (which greatly limit the possible influence of the well-understood gradient-driven hydrotropic response), our results show that 1) individual roots as well as the root system as a whole adapt to the pattern of water availability to maximize access to water, and that 2) this adaptation increases as water sources become more rare. These results suggest that either plant roots are more sensitive to water gradients than humanmade water sensors by 3-5 orders of magnitude, or they might have developed, like other organisms, mechanisms for water foraging that allow them to find water in the absence of an external gradient in water potential.

Intricate genetic variation networks control the adventitious root growth angle in apple

Background

The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified in crops. However, the underlying mechanisms of the RGA remain poorly understood, especially in apple rootstocks. The objective of this study was to identify QTLs, validate genetic variation networks, and develop molecular markers for the RGA in apple rootstock.

Results

Bulked segregant analysis by sequencing (BSA-seq) identified 25 QTLs for RGA using 1955 hybrids of the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., large RGA) and ‘M9’ (M. pumila Mill., small RGA). With RNA sequencing (RNA-seq) and parental resequencing, six major functional genes were identified and constituted two genetic variation networks for the RGA. Two single nucleotide polymorphisms (SNPs) of the MdLAZY1 promoter damaged the binding sites of MdDREB2A and MdHSFB3, while one SNP of MdDREB2A and MdIAA1 affected the interactions of MdDREB2A/MdHSFB3 and MdIAA1/MdLAZY1, respectively. A SNP within the MdNPR5 promoter damaged the interaction between MdNPR5 and MdLBD41, while one SNP of MdLBD41 interrupted the MdLBD41/MdbHLH48 interaction that affected the binding ability of MdLBD41 on the MdNPR5 promoter. Twenty six SNP markers were designed on candidate genes in each QTL interval, and the marker effects varied from 0.22°-26.11°.

Conclusions

Six diagnostic markers, SNP592, G122, b13, Z312, S1272, and S1288, were used to identify two intricate genetic variation networks that control the RGA and may provide new insights into the accuracy of the molecular markers. The QTLs and SNP markers can potentially be used to select deep-rooted apple rootstocks.

The Importance of Earth Reference Controls in Spaceflight -Omics Research: Characterization of Nucleolin Mutants from the Seedling Growth Experiments

Understanding plant adaptive responses to the space environment is a requisite for enabling space farming. Spaceflight produces deleterious effects on plant cells, particularly affecting ribosome biogenesis, a complex stress-sensitive process coordinated with cell division and differentiation, known to be activated by red light. Here, in a series of ground studies, we have used mutants from the two Arabidopsis nucleolin genes (NUC1 and NUC2, nucleolar regulators of ribosome biogenesis) to better understand their role in adaptive response mechanisms to stress on Earth. Thus, we show that nucleolin stress-related gene NUC2 can compensate for the environmental stress provided by darkness in nuc1 plants, whereas nuc2 plants are not able to provide a complete response to red light. These ground control findings, as part of the ESA/NASA Seedling Growth spaceflight experiments, will determine the basis for the identification of genetic backgrounds enabling an adaptive advantage for plants in future space experiments.

A Positive Tropism of Rice Roots toward a Nutrient Source

Plants take up water and nutrients through roots, and uptake efficiency depends on root behavior. Roots recognize the moisture gradient in the soil and grow toward the direction of high moisture. This phenomenon is called hydrotropism, and it contributes to efficient water uptake. As nutrients in soil are also unevenly distributed, it is beneficial for plants to grow their roots in the direction of increasing nutrient concentrations, but such a phenomenon has not been demonstrated. Here, we describe the directional growth of roots in response to a nutrient gradient. Using our assay system, the gradient of a nitrogen nutrient, NH4+, was sufficient to stimulate positive tropic responses of rice lateral roots. This phenomenon is a tropism of plant roots to nutrients; hence, we propose the name 'nutritropism'. As well as other tropisms, differential cell elongation was observed before the elongation zone during nutritropism, but the pattern promoting cell elongation preferentially on the non-stimulated side was opposite to those in root hydrotropism and gravitropism. Our evaluation of the NH4+ gradient suggested that the root tips responded to a sub-micromolar difference in NH4+ concentration on both sides of the root. Hydrotropism, gravitropism and phototropism were described in plants as the 'power of movement' by Charles and Francis Darwin in 1880, and these three tropisms have attracted the attention of plant scientists for more than 130 years. Our discovery of nutritropism represents the fourth 'power of movement' in plants and provides a novel root behavioral property used by plants to acquire nutrients efficiently.

Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato

Dissecting the genetic regulation of gene expression is critical for understanding phenotypic variation and species evolution. However, our understanding of the transcriptional variability in sweet potato remains limited. Here, we analyzed two publicly available datasets to explore the landscape of transcriptomic variations and its genetic basis in the storage roots of sweet potato. The comprehensive analysis identified a total of 724,438 high-confidence single nucleotide polymorphisms (SNPs) and 26,026 expressed genes. Expression quantitative trait locus (eQTL) analysis revealed 4408 eQTLs regulating the expression of 3646 genes, including 2261 local eQTLs and 2147 distant eQTLs. Two distant eQTL hotspots were found with target genes significantly enriched in specific functional classifications. By combining the information from regulatory network analyses, eQTLs and association mapping, we found that IbMYB1-2 acts as a master regulator and is the major gene responsible for the activation of anthocyanin biosynthesis in the storage roots of sweet potato. Our study provides the first insight into the genetic architecture of genome-wide expression variation in sweet potato and can be used to investigate the potential effects of genetic variants on key agronomic traits in sweet potato.

RNA-seq analyses of Arabidopsis thaliana seedlings after exposure to blue-light phototropic stimuli in microgravity

PREMISE

Plants synthesize information from multiple environmental stimuli when determining their direction of growth. Gravity, being ubiquitous on Earth, plays a major role in determining the direction of growth and overall architecture of the plant. Here, we utilized the microgravity environment on board the International Space Station (ISS) to identify genes involved influencing growth and development of phototropically stimulated seedlings of Arabidopsis thaliana.

METHODS

Seedlings were grown on the ISS, and RNA was extracted from 7 samples (pools of 10-15 plants) grown in microgravity (μg) or Earth gravity conditions (1-g). Transcriptomic analyses via RNA sequencing (RNA-seq) of differential gene expression was performed using the HISAT2-Stringtie-DESeq2 RNASeq pipeline. Differentially expressed genes were further characterized by using Pathway Analysis and enrichment for Gene Ontology classifications.

RESULTS

For 296 genes that were found significantly differentially expressed between plants in microgravity compared to 1-g controls, Pathway Analysis identified eight molecular pathways that were significantly affected by reduced gravity conditions. Specifically, light-associated pathways (e.g., photosynthesis-antenna proteins, photosynthesis, porphyrin, and chlorophyll metabolism) were significantly downregulated in microgravity.

CONCLUSIONS

Gene expression in A. thaliana seedlings grown in microgravity was significantly altered compared to that of the 1-g control. Understanding how plants grow in conditions of microgravity not only aids in our understanding of how plants grow and respond to the environment but will also help to efficiently grow plants during long-range space missions.

Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana

BACKGROUND

Root morphology is known to be affected by light quality, quantity and direction. Light signal is perceived at the shoot, translocated to roots through vasculature and further modulates the root development. Photoreceptors are differentially expressed in both shoot and root cells. The light irradiation to the root affects shoot morphology as well as whole plant development. The current work aims to understand the white light intensity dependent changes in root patterning and correlate that with the global gene expression profile.

RESULTS

Different fluence of white light (WL) regulate overall root development via modulating the expression of a specific set of genes. Phytochrome A deficient Arabidopsis thaliana (phyA-211) showed shorter primary root compared to phytochrome B deficient (phyB-9) and wild type (WT) seedlings at a lower light intensity. However, at higher intensity, both mutants showed shorter primary root in comparison to WT. The lateral root number was observed to be lowest in phyA-211 at intensities of 38 and 75 μmol m ^- 2 s ^- 1. The number of adventitious roots was significantly lower in phyA-211 as compared to WT and phyB-9 under all light intensities tested. With the root phenotypic data, microarray was performed for four different intensities of WL light in WT. Here, we identified ~ 5243 differentially expressed genes (DEGs) under all light intensities. Gene ontology-based analysis indicated that different intensities of WL predominantly affect a subset of genes having catalytic activity and localized to the cytoplasm and membrane. Furthermore, when root is irradiated with different intensities of WL, several key genes involved in hormone, light signaling and clock-regulated pathways are differentially expressed.

CONCLUSION

Using genome wide microarray-based approach, we have identified candidate genes in Arabidopsis root that responded to the changes in light intensities. Alteration in expression of genes such as PIF4, COL9, EPR1, CIP1, ARF18, ARR6, SAUR9, TOC1 etc. which are involved in light, hormone and clock pathway was validated by qRT-PCR. This indicates their potential role in light intensity mediated root development.

Light and auxin signaling cross-talk programme root development in plants

Root development in plants is affected by light and phytohormones. Different ranges of light wavelength influence root patterning in a particular manner. Red and white light promote overall root development, whereas blue light has both positive as well as negative role in these processes. Light-mediated root development primarily occurs through modulation of synthesis, signaling and transport of the phytohormone auxin. Auxin has been shown to play a critical role in root development. It is being well-understood that components of light and auxin signaling cross-talk with each other. However, the signaling network that can modulate the root development is an intense area of research. Currently, limited information is available about the interaction of these two signaling pathways. This review not only summarizes the current findings on how different quality and quantity of light affect various aspects of root development but also present the role of auxin in these developmental aspects starting from lower to higher plants.

Root Tropisms: Investigations on Earth and in Space to Unravel Plant Growth Direction

Root tropisms are important responses of plants, allowing them to adapt their growth direction. Research on plant tropisms is indispensable for future space programs that envisage plant-based life support systems for long-term missions and planet colonization. Root tropisms encompass responses toward or away from different environmental stimuli, with an underexplored level of mechanistic divergence. Research into signaling events that coordinate tropistic responses is complicated by the consistent coincidence of various environmental stimuli, often interacting via shared signaling mechanisms. On Earth the major determinant of root growth direction is the gravitational vector, acting through gravitropism and overruling most other tropistic responses to environmental stimuli. Critical advancements in the understanding of root tropisms have been achieved nullifying the gravitropic dominance with experiments performed in the microgravity environment. In this review, we summarize current knowledge on root tropisms to different environmental stimuli. We highlight that the term tropism must be used with care, because it can be easily confused with a change in root growth direction due to asymmetrical damage to the root, as can occur in apparent chemotropism, electrotropism, and magnetotropism. Clearly, the use of Arabidopsis thaliana as a model for tropism research contributed much to our understanding of the underlying regulatory processes and signaling events. However, pronounced differences in tropisms exist among species, and we argue that these should be further investigated to get a more comprehensive view of the signaling pathways and sensors. Finally, we point out that the Cholodny-Went theory of asymmetric auxin distribution remains to be the central and unifying tropistic mechanism after 100 years. Nevertheless, it becomes increasingly clear that the theory is not applicable to all root tropistic responses, and we propose further research to unravel commonalities and differences in the molecular and physiological processes orchestrating root tropisms.

Quantitative dissection of variations in root growth rate: a matter of cell proliferation or of cell expansion?

Plant organ growth results from cell production and cell expansion. Deciphering the contribution of each of these processes to growth rate is an important issue in developmental biology. Here, we investigated the cellular processes governing root elongation rate, considering two sources of variation: genotype and disturbance by chemicals (NaCl, polyethylene glycol, H2O2, abscisic acid). Exploiting the adventitious rooting capacity of the Populus genus, and using time-lapse imaging under infrared-light, particle image velocimetry, histological analysis, and kinematics, we quantified the cellular processes involved in root growth variation, and analysed the covariation patterns between growth parameters. The rate of cell production by the root apical meristem and the number of dividing cells were estimated in vivo without destructive measurement. We found that the rate of cell division contributed more to the variation in cell production rate than the number of dividing cells. Regardless of the source of variation, the length of the elongation zone was the best proxy for growth rate, summarizing rates of cell production and cell elongation into a single parameter. Our results demonstrate that cell production rate is the main driver of growth rate, whereas elemental elongation rate is a key driver of short-term growth adjustments.

The combined effects of real or simulated microgravity and red-light photoactivation on plant root meristematic cells

Red light is able to compensate for deleterious effects of microgravity on root cell growth and proliferation. Partial gravity combined with red light produces differential signals during the early plant development. Light and gravity are environmental cues used by plants throughout evolution to guide their development. We have investigated the cross-talk between phototropism and gravitropism under altered gravity in space. The focus was on the effects on the meristematic balance between cell growth and proliferation, which is disrupted under microgravity in the dark. In our spaceflight experiments, seedlings of three Arabidopsis thaliana genotypes, namely the wild type and mutants of phytochrome A and B, were grown for 6 days, including red-light photoactivation for the last 2 days. Apart from the microgravity and the 1g on-board control conditions, fractional gravity (nominally 0.1g, 0.3g, and 0.5g) was created with on-board centrifuges. In addition, a simulated microgravity (random positioning machine, RPM) experiment was performed on ground, including both dark-grown and photostimulated samples. Photoactivated samples in spaceflight and RPM experiments showed an increase in the root length consistent with phototropic response to red light, but, as gravity increased, a gradual decrease in this response was observed. Uncoupling of cell growth and proliferation was detected under microgravity in darkness by transcriptomic and microscopic methods, but red-light photoactivation produced a significant reversion. In contrast, the combination of red light and partial gravity produced small but consistent variations in the molecular markers of cell growth and proliferation, suggesting an antagonistic effect between light and gravity signals at the early plant development. Understanding these parameters of plant growth and development in microgravity will be important as bioregenerative life support systems for the colonization of the Moon and Mars.

Entrainment of Arabidopsis roots to the light:dark cycle by light piping

Correct operation of the plant circadian clock is crucial for optimal growth and development. Recent evidence has shown that the plant clock is tissue specific and potentially hierarchical, implying that there are signalling mechanisms that can synchronise the clock in different tissues. Here, I have addressed the mechanism that allows the shoot and root clocks to be synchronised in light:dark cycles but not in continuous light. Luciferase imaging data from 2 different Arabidopsis accessions with 2 different markers show that the period of the root clock is much less sensitive to blue light than to red light. Decapitated roots were imaged either in darkness or with the top section of root tissue exposed to light. Exposure to red light reduced the period of the root tissue maintained in darkness, whereas exposure to blue light did not. The data indicate that light can be piped through root tissue to affect the circadian period of tissue in darkness. I propose that the synchronisation of shoots and roots in light:dark cycles is achieved by light piping from shoots to roots.

Phytochrome and Phytohormones: Working in Tandem for Plant Growth and Development

Being sessile organisms, plants need to continually adapt and modulate their rate of growth and development in accordance with the changing environmental conditions, a phenomenon referred to as plasticity. Plasticity in plants is a highly complex process that involves a well-coordinated interaction between different signaling pathways, the spatiotemporal involvement of phytohormones and cues from the environment. Though research studies are being carried out over the years to understand how plants perceive the signals from changing environmental conditions and activate plasticity, such remain a mystery to be resolved. Among all environmental cues, the light seems to be the stand out factor influencing plant growth and development. During the course of evolution, plants have developed well-equipped signaling system that enables regulation of both quantitative and qualitative differences in the amount of perceived light. Light influences essential developmental switches in plants ranging from germination or transition to flowering, photomorphogenesis, as well as switches in response to shade avoidances and architectural changes occurring during phototropism. Abscisic acid (ABA) is controlling seed germination and is regulated by light. Furthermore, circadian clock adds another level of regulation to plant growth by integrating light signals with different hormonal pathways. MYB96 has been identified as a regulator of circadian gating of ABA-mediated responses in plants by binding to the TIMING OF CAB EXPRESSION 1(TOC1) promoter. This review will present a representative regulatory model, highlight the successes achieved in employing novel strategies to dissect the levels of interaction and provide perspective for future research on phytochrome-phytohormones relationships toward facilitating plant growth, development, and function under abiotic-biotic stresses.

Phenotyping roots in darkness: disturbance-free root imaging with near infrared illumination

Root systems architecture (RSA) and size properties are essential determinants of plant performance and need to be assessed in high-throughput plant phenotyping platforms. Thus, we tested a concept that involves near-infrared (NIR) imaging of roots growing along surfaces of transparent culture vessels using special long pass filters to block their exposure to visible light. Two setups were used to monitor growth of Arabidopsis, rapeseed, barley and maize roots upon exposure to white light, filter-transmitted radiation or darkness: root growth direction was analysed (1) through short-term cultivation on agar plates, and (2) using soil-filled transparent pots to monitor long-term responses. White light-triggered phototropic responses were detected for Arabidopsis in setup 1, and for rapeseed, barley and maize roots in setups 1 and 2, whereas light effects could be avoided by use of the NIR filter thus confirming its suitability to mimic darkness. NIR image-derived 'root volume' values correlated well with root dry weight. The root system fractions visible at the different pot sides and in different zones revealed species- and genotype-dependent variation of spatial root distribution and other RSA traits. Following this validated concept, root imaging setups may be integrated into shoot phenotyping facilities in order to enable root system analysis in the context of whole-plant performance investigations.

Light Signaling, Root Development, and Plasticity

Light signaling can affect root development and plasticity, either directly or through shoot-root communication via sugars, hormones, light, or other mobile factors.

Differential response of Scots pine seedlings to variable intensity and ratio of red and far-red light

We investigated the response to increasing intensity of red (R) and far-R (FR) light and to a decrease in R:FR ratio in Pinus sylvestris L. (Scots pine) seedling. The results showed that FR high-irradiance response for hypocotyl elongation may be present in Scots pine and that this response is enhanced by increasing light intensity. However, both hypocotyl inhibition and pigment accumulation were more strongly affected by the R light compared with FR light. This is in contrast to previous reports in Arabidopsis thaliana (L.) Heynh. In the angiosperm, A. thaliana R light shows an overall milder effect on inhibition of hypocotyl elongation and on pigment biosynthesis compared with FR suggesting conifers and angiosperms respond very differently to the different light regimes. Scots pine shade avoidance syndrome with longer hypocotyls, shorter cotyledons and lower chlorophyll content in response to shade conditions resembles the response observed in A. thaliana. However, anthocyanin accumulation increased with shade in Scots pine, which again differs from what is known in angiosperms. Overall, the response of seedling development and physiology to R and FR light in Scots pine indicates that the regulatory mechanism for light response may differ between gymnosperms and angiosperms.

Striking the Right Chord: Signaling Enigma during Root Gravitropism

Plants being sessile can often be judged as passive acceptors of their environment. However, plants are actually even more active in responding to the factors from their surroundings. Plants do not have eyes, ears or vestibular system like animals, still they "know" which way is up and which way is down? This is facilitated by receptor molecules within plant which perceive changes in internal and external conditions such as light, touch, obstacles; and initiate signaling pathways that enable the plant to react. Plant responses that involve a definite and specific movement are called "tropic" responses. Perhaps the best known and studied tropisms are phototropism, i.e., response to light, and geotropism, i.e., response to gravity. A robust root system is vital for plant growth as it can provide physical anchorage to soil as well as absorb water, nutrients and essential minerals from soil efficiently. Gravitropic responses of both primary as well as lateral root thus become critical for plant growth and development. The molecular mechanisms of root gravitropism has been delved intensively, however, the mechanism behind how the potential energy of gravity stimulus converts into a biochemical signal in vascular plants is still unknown, due to which gravity sensing in plants still remains one of the most fascinating questions in molecular biology. Communications within plants occur through phytohormones and other chemical substances produced in plants which have a developmental or physiological effect on growth. Here, we review current knowledge of various intrinsic signaling mechanisms that modulate root gravitropism in order to point out the questions and emerging developments in plant directional growth responses. We are also discussing the roles of sugar signals and their interaction with phytohormone machinery, specifically in context of root directional responses.

The foundations of plant intelligence

Intelligence is defined for wild plants and its role in fitness identified. Intelligent behaviour exhibited by single cells and systems similarity between the interactome and connectome indicates neural systems are not necessary for intelligent capabilities. Plants sense and respond to many environmental signals that are assessed to competitively optimize acquisition of patchily distributed resources. Situations of choice engender motivational states in goal-directed plant behaviour; consequent intelligent decisions enable efficient gain of energy over expenditure. Comparison of swarm intelligence and plant behaviour indicates the origins of plant intelligence lie in complex communication and is exemplified by cambial control of branch function. Error correction in behaviours indicates both awareness and intention as does the ability to count to five. Volatile organic compounds are used as signals in numerous plant interactions. Being complex in composition and often species and individual specific, they may represent the plant language and account for self and alien recognition between individual plants. Game theory has been used to understand competitive and cooperative interactions between plants and microbes. Some unexpected cooperative behaviour between individuals and potential aliens has emerged. Behaviour profiting from experience, another simple definition of intelligence, requires both learning and memory and is indicated in the priming of herbivory, disease and abiotic stresses.

The foundations of plant intelligence

Intelligence is defined for wild plants and its role in fitness identified. Intelligent behaviour exhibited by single cells and systems similarity between the interactome and connectome indicates neural systems are not necessary for intelligent capabilities. Plants sense and respond to many environmental signals that are assessed to competitively optimize acquisition of patchily distributed resources. Situations of choice engender motivational states in goal-directed plant behaviour; consequent intelligent decisions enable efficient gain of energy over expenditure. Comparison of swarm intelligence and plant behaviour indicates the origins of plant intelligence lie in complex communication and is exemplified by cambial control of branch function. Error correction in behaviours indicates both awareness and intention as does the ability to count to five. Volatile organic compounds are used as signals in numerous plant interactions. Being complex in composition and often species and individual specific, they may represent the plant language and account for self and alien recognition between individual plants. Game theory has been used to understand competitive and cooperative interactions between plants and microbes. Some unexpected cooperative behaviour between individuals and potential aliens has emerged. Behaviour profiting from experience, another simple definition of intelligence, requires both learning and memory and is indicated in the priming of herbivory, disease and abiotic stresses.

[Tropisms in underground shoots — stolons and rhizomes]

In the review, the problem of plant movements (photo- and gravitropism) is discussed. The contemporary data on physiological and molecular mechanisms of tropisms in underground shoots and roots are presented. Special attention is paid to diagravitropism phenomenon in underground shoots (stolons and rhizomes) that grow in perpendicular direction to the Earth's gravitational axis. The role of phytochrome control in maintaining the horizontal growth of stolons and rhizomes is demonstrated, and physiological mechanisms of photo- and diagravitropism are discussed. It is shown that switching of an underground shoot tip from diatropic to ortotropic (vertical) growth is dependent on the carbohydrate and phytohor-mone balance. The perspectives are outlined for further exploratory studies on mechanisms of growth orientation and morphogenesis of underground diagravitropic shoots.

Comparative Transcriptome Analysis Reveal Candidate Genes Potentially Involved in Regulation of Primocane Apex Rooting in Raspberry (Rubus spp.)

Raspberries (Rubus spp.) exhibit a unique rooting process that is initiated from the stem apex of primocane, conferring an unusual asexual mode of reproduction to this plant. However, the full complement of genes involved in this process has not been identified. To this end, the present study analyzed the transcriptomes of the Rubus primocane and floricane stem apex at three developmental stages by Digital Gene Expression profiling to identify genes that regulate rooting. Sequencing and de novo assembly yielded 26.82 Gb of nucleotides and 59,173 unigenes; 498, 7,346, 4,110, 7,900, 9,397, and 4,776 differently expressed genes were identified in paired comparisons of SAF1 (floricane at developmental stage 1) vs. SAP1 (primocane at developmental stage 1), SAF2 vs. SAP2, SAF3 vs. SAP3, SAP1 vs. SAP2, SAP1 vs. SAP3, and SAP2 vs. SAP3, respectively. SAP1 maintains an extension growth pattern; SAP2 then exhibits growth arrest and vertical (downward) gravitropic deflection; and finally, short roots begin to form on the apex of SAP3. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis of SAP1 vs. SAP2 revealed 12 pathways that were activated in response to shoot growth arrest and root differentiation, including circadian rhythm-plant (ko04712) and plant hormone signal transduction (ko04075). Our results indicate that genes related to circadian rhythm, ethylene and auxin signaling, shoot growth, and root development are potentially involved in the regulation of primocane apex rooting in Rubus. These findings provide a basis for elucidating the molecular mechanisms of primocane apex rooting in this economically valuable crop.

A novel blue-light phototropic response is revealed in roots of Arabidopsis thaliana in microgravity

Blue-light positive phototropism in roots is masked by gravity and revealed in conditions of microgravity. In addition, the magnitude of red-light positive phototropic curvature is correlated to the magnitude of gravity. Due to their sessile nature, plants utilize environmental cues to grow and respond to their surroundings. Two of these cues, light and gravity, play a substantial role in plant orientation and directed growth movements (tropisms). However, very little is currently known about the interaction between light- (phototropic) and gravity (gravitropic)-mediated growth responses. Utilizing the European Modular Cultivation System on board the International Space Station, we investigated the interaction between phototropic and gravitropic responses in three Arabidopsis thaliana genotypes, Landsberg wild type, as well as mutants of phytochrome A and phytochrome B. Onboard centrifuges were used to create a fractional gravity gradient ranging from reduced gravity up to 1g. A novel positive blue-light phototropic response of roots was observed during conditions of microgravity, and this response was attenuated at 0.1g. In addition, a red-light pretreatment of plants enhanced the magnitude of positive phototropic curvature of roots in response to blue illumination. In addition, a positive phototropic response of roots was observed when exposed to red light, and a decrease in response was gradual and correlated with the increase in gravity. The positive red-light phototropic curvature of hypocotyls when exposed to red light was also confirmed. Both red-light and blue-light phototropic responses were also shown to be affected by directional light intensity. To our knowledge, this is the first characterization of a positive blue-light phototropic response in Arabidopsis roots, as well as the first description of the relationship between these phototropic responses in fractional or reduced gravities.

Flavonols Mediate Root Phototropism and Growth through Regulation of Proliferation-to-Differentiation Transition

Roots normally grow in darkness, but they may be exposed to light. After perceiving light, roots bend to escape from light (root light avoidance) and reduce their growth. How root light avoidance responses are regulated is not well understood. Here, we show that illumination induces the accumulation of flavonols in Arabidopsis thaliana roots. During root illumination, flavonols rapidly accumulate at the side closer to light in the transition zone. This accumulation promotes asymmetrical cell elongation and causes differential growth between the two sides, leading to root bending. Furthermore, roots illuminated for a long period of time accumulate high levels of flavonols. This high flavonol content decreases both auxin signaling and PLETHORA gradient as well as superoxide radical content, resulting in reduction of cell proliferation. In addition, cytokinin and hydrogen peroxide, which promote root differentiation, induce flavonol accumulation in the root transition zone. As an outcome of prolonged light exposure and flavonol accumulation, root growth is reduced and a different root developmental zonation is established. Finally, we observed that these differentiation-related pathways are required for root light avoidance. We propose that flavonols function as positional signals, integrating hormonal and reactive oxygen species pathways to regulate root growth direction and rate in response to light.

Spatiotemporal Phytochrome Signaling during Photomorphogenesis: From Physiology to Molecular Mechanisms and Back

Light exposure results in distinct responses in specific seedling tissues during photomorphogenesis. Light promotes growth of cotyledons and leaves, as well as development and elongation of roots, whereas light inhibits elongation of hypocotyls. For distinct plant responses such as shade avoidance, far-red light or shifts in spectral light quality similarly have disparate impacts on distinct plant tissues, resulting in elongation of stems or petioles and a reduction in growth of leaf blades for many species. The physiological bases of such tissue- and organ-specific light responses were initially studied using localized irradiation of specific tissues and organs, or irradiation of dissected plant parts. These historical approaches were used to identify spatial-specific pools of photoreceptors responsible for regulating local, i.e., tissue- or organ-specific, or distal, i.e., interorgan, plant responses. The red/far-red responsive phytochromes have been the most widely studied among photoreceptors in this regard. Whereas, the spatial localization of photoreceptors regulating many tissue- or organ-specific light responses were identified, the underlying signaling networks responsible for mediating the observed responses have not been well defined. Recent approaches used to investigate the molecular bases of spatiotemporal light responses include selective irradiation of plants harboring mutations in specific photoreceptors, tissue-specific expression of photoreceptors, primarily in photoreceptor mutant backgrounds, or tissue-specific biochemical ablation of photoreceptor accumulation. Progressive integration of such approaches for regulating the availability of localized pools of phytochromes with the use of transcriptomic or proteomic analyses for assessing the genes or proteins which these spatially discrete pools of phytochrome regulate is yielding emergent insight into the molecular bases of spatiotemporal phytochrome signaling pathways responsible for regulating spatiotemporal light responses of which we have been aware of at the physiological level for decades. Here, I discuss historical and emerging approaches to elucidating spatiotemporal signaling mediated by phytochromes during photomorphogenesis.

Genetic control of root growth: from genes to networks

BACKGROUND

Roots are essential organs for higher plants. They provide the plant with nutrients and water, anchor the plant in the soil, and can serve as energy storage organs. One remarkable feature of roots is that they are able to adjust their growth to changing environments. This adjustment is possible through mechanisms that modulate a diverse set of root traits such as growth rate, diameter, growth direction and lateral root formation. The basis of these traits and their modulation are at the cellular level, where a multitude of genes and gene networks precisely regulate development in time and space and tune it to environmental conditions.

SCOPE

This review first describes the root system and then presents fundamental work that has shed light on the basic regulatory principles of root growth and development. It then considers emerging complexities and how they have been addressed using systems-biology approaches, and then describes and argues for a systems-genetics approach. For reasons of simplicity and conciseness, this review is mostly limited to work from the model plant Arabidopsis thaliana, in which much of the research in root growth regulation at the molecular level has been conducted.

CONCLUSIONS

While forward genetic approaches have identified key regulators and genetic pathways, systems-biology approaches have been successful in shedding light on complex biological processes, for instance molecular mechanisms involving the quantitative interaction of several molecular components, or the interaction of large numbers of genes. However, there are significant limitations in many of these methods for capturing dynamic processes, as well as relating these processes to genotypic and phenotypic variation. The emerging field of systems genetics promises to overcome some of these limitations by linking genotypes to complex phenotypic and molecular data using approaches from different fields, such as genetics, genomics, systems biology and phenomics.

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

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

Roles of proteome dynamics and cytokinin signaling in root to hypocotyl ratio changes induced by shading roots of Arabidopsis seedlings

In nature, root systems of most terrestrial plants are protected from light exposure by growing in a dark soil environment. Hence, in vitro cultivation in transparent Petri dishes leads to physiological perturbations, but the mechanisms underlying root-mediated light perception and responses have not been fully elucidated. Thus, we compared Arabidopsis thaliana seedling development in transparent and darkened Petri dishes at low light intensity (20 µmol m(-2) s(-1)), allowing us to follow (inter alia) hypocotyl elongation, which is an excellent process for studying interactions of signals involved in the regulation of growth and developmental responses. To obtain insights into molecular events underlying differences in seedling growth under these two conditions, we employed liquid chromatography-mass spectrometry (LC-MS) shotgun proteomics (available via the PRIDE deposit PXD001612). In total, we quantified the relative abundances of peptides representing 1,209 proteins detected in all sample replicates of LC-MS analyses. Comparison of MS spectra after manual validation revealed 48 differentially expressed proteins. Functional classification, analysis of available gene expression data and literature searches revealed alterations associated with root illumination (inter alia) in autotrophic CO2 fixation, C compound and carbohydrate metabolism, and nitrogen metabolism. The results also indicate a previously unreported role for cytokinin plant hormones in the escape-tropism response to root illumination. We complemented these results with reverse transcription followed by quantitative PCR (RT-qPCR), chlorophyll fluorescence and detailed cytokinin signaling analyses, detecting in the latter a significant increase in the activity of the cytokinin two-component signaling cascade in roots and implicating the cytokinin receptor AHK3 as the major mediator of root to hypocotyl signaling in responses to root illumination.

Genetic improvement for root growth angle to enhance crop production

The root system is an essential organ for taking up water and nutrients and anchoring shoots to the ground. On the other hand, the root system has rarely been regarded as breeding target, possibly because it is more laborious and time-consuming to evaluate roots (which require excavation) in a large number of plants than aboveground tissues. The root growth angle (RGA), which determines the direction of root elongation in the soil, affects the area in which roots capture water and nutrients. In this review, we describe the significance of RGA as a potential trait to improve crop production, and the physiological and molecular mechanisms that regulate RGA. We discuss the prospects for breeding to improve RGA based on current knowledge of quantitative trait loci for RGA in rice.

Underground tuning: quantitative regulation of root growth

Plants display a high degree of phenotypic plasticity that allows them to tune their form and function to changing environments. The plant root system has evolved mechanisms to anchor the plant and to efficiently explore soils to forage for soil resources. Key to this is an enormous capacity for plasticity of multiple traits that shape the distribution of roots in the soil. Such root system architecture-related traits are determined by root growth rates, root growth direction, and root branching. In this review, we describe how the root system is constituted, and which mechanisms, pathways, and genes mainly regulate plasticity of the root system in response to environmental variation.

How and why do root apices sense light under the soil surface?

Light can penetrate several centimeters below the soil surface. Growth, development and behavior of plant roots are markedly affected by light despite their underground lifestyle. Early studies provided contrasting information on the spatial and temporal distribution of light-sensing cells in the apical region of root apex and discussed the physiological roles of plant hormones in root responses to light. Recent biological and microscopic advances have improved our understanding of the processes involved in the sensing and transduction of light signals, resulting in subsequent physiological and behavioral responses in growing root apices. Here, we review current knowledge of cellular distributions of photoreceptors and their signal transduction pathways in diverse root tissues and root apex zones. We are discussing also the roles of auxin transporters in roots exposed to light, as well as interactions of light signal perceptions with sensing of other environmental factors relevant to plant roots.

Light and gravity signals synergize in modulating plant development

Tropisms are growth-mediated plant movements that help plants to respond to changes in environmental stimuli. The availability of water and light, as well as the presence of a constant gravity vector, are all environmental stimuli that plants sense and respond to via directed growth movements (tropisms). The plant response to gravity (gravitropism) and the response to unidirectional light (phototropism) have long been shown to be interconnected growth phenomena. Here, we discuss the similarities in these two processes, as well as the known molecular mechanisms behind the tropistic responses. We also highlight research done in a microgravity environment in order to decouple two tropisms through experiments carried out in the absence of a significant unilateral gravity vector. In addition, alteration of gravity, especially the microgravity environment, and light irradiation produce important effects on meristematic cells, the undifferentiated, highly proliferating, totipotent cells which sustain plant development. Microgravity produces the disruption of meristematic competence, i.e., the decoupling of cell proliferation and cell growth, affecting the regulation of the cell cycle and ribosome biogenesis. Light irradiation, especially red light, mediated by phytochromes, has an activating effect on these processes. Phytohormones, particularly auxin, also are key mediators in these alterations. Upcoming experiments on the International Space Station will clarify some of the mechanisms and molecular players of the plant responses to these environmental signals involved in tropisms and the cell cycle.

Root growth movements: waving and skewing

Roots anchor a plant in the soil, acquire nutrition and respond to environmental cues. Roots perform these functions using intricate movements and a variety of pathways have been implicated in mediating their growth patterns. These include endogenous genetic factors, perception of multiple environmental stimuli, signaling pathways interacting with hormonal dynamics and cellular processes of rapid cell elongation. In this review we attempt to consolidate our understanding of two specific types of root movements, waving and skewing, that arise on the surface of growth media, and how they are regulated by various genes and factors. These include crucial factors that are part of a complex nexus of processes including polar auxin transport and cytoskeletal dynamics. This knowledge can be extrapolated in the future for engineering plants with root architecture better suited for different soil and growth conditions such as abiotic stresses or even extended spaceflight. Technological innovations and interdisciplinary approaches promise to allow the tracking of root movements on a much finer scale, thus helping to expedite the discovery of more nodes in the regulation of root waving and skewing and movement in general.

Accumulation of TIP2;2 Aquaporin during Dark Adaptation Is Partially PhyA Dependent in Roots of Arabidopsis Seedlings

Light regulates the expression and function of aquaporins, which are involved in water and solute transport. In Arabidopsis thaliana, mRNA levels of one of the aquaporin genes, TIP2;2, increase during dark adaptation and decrease under far-red light illumination, but the effects of light at the protein level and on the mechanism of light regulation remain unknown. Numerous studies have described the light regulation of aquaporin genes, but none have identified the regulatory mechanisms behind this regulation via specific photoreceptor signaling. In this paper, we focus on the role of phytochrome A (phyA) signaling in the regulation of the TIP2;2 protein. We generated Arabidopsis transgenic plants expressing a TIP2;2-GFP fusion protein driven by its own promoter, and showed several differences in TIP2;2 behavior between wild type and the phyA mutant. Fluorescence of TIP2;2-GFP protein in the endodermis of roots in the wild-type seedlings increased during dark adaptation, but not in the phyA mutant. The amount of the TIP2;2-GFP protein in wild-type seedlings decreased rapidly under far-red light illumination, and a delay in reduction of TIP2;2-GFP was observed in the phyA mutant. Our results imply that phyA, cooperating with other photoreceptors, modulates the level of TIP2;2 in Arabidopsis roots.

Plant biology in reduced gravity on the Moon and Mars

While there have been numerous studies on the effects of microgravity on plant biology since the beginning of the Space Age, our knowledge of the effects of reduced gravity (less than the Earth nominal 1 g) on plant physiology and development is very limited. Since international space agencies have cited manned exploration of Moon/Mars as long-term goals, it is important to understand plant biology at the lunar (0.17 g) and Martian levels of gravity (0.38 g), as plants are likely to be part of bioregenerative life-support systems on these missions. First, the methods to obtain microgravity and reduced gravity such as drop towers, parabolic flights, sounding rockets and orbiting spacecraft are reviewed. Studies on gravitaxis and gravitropism in algae have suggested that the threshold level of gravity sensing is around 0.3 g or less. Recent experiments on the International Space Station (ISS) showed attenuation of phototropism in higher plants occurs at levels ranging from 0.l g to 0.3 g. Taken together, these studies suggest that the reduced gravity level on Mars of 0.38 g may be enough so that the gravity level per se would not be a major problem for plant development. Studies that have directly considered the impact of reduced gravity and microgravity on bioregenerative life-support systems have identified important biophysical changes in the reduced gravity environments that impact the design of these systems. The author suggests that the current ISS laboratory facilities with on-board centrifuges should be used as a test bed in which to explore the effects of reduced gravity on plant biology, including those factors that are directly related to developing life-support systems necessary for Moon and Mars exploration.

Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes

The transcriptome of seedlings was analyzed from experiments performed on the International Space Station to study the interacting effects of light and gravity on plant tropisms (project named TROPI-2; Kiss et al. 2012). Seeds of Arabidopsis were germinated in space, and seedlings were then grown in the European Modular Cultivation System for 4 days at ~1g followed by exposure to a range of gravitational accelerations (from microgravity to 1g) and two light treatments (blue light with or without a 1 h pretreatment with red). At the end of the experiments, the cassettes containing the seedlings were frozen in the minus eighty laboratory freezer and returned to Earth on space shuttle mission STS-131. The RNA was extracted from whole seedlings and used for the transcriptome analyses. A comparison of 1g spaceflight samples with 1g ground controls identified 230 genes that were differentially regulated at least twofold, emphasizing the need for "in situ" tissue fixation on a 1g centrifuge as an important control for spaceflight experiments. A further comparison of all spaceflight samples with ground controls identified approximately 280 genes that were differentially regulated at least twofold. Of these genes, several were involved in regulating cell polarity (i.e., auxin, calcium, lipid metabolism), cell-wall development, oxygen status, and cell defense or stress. However, when the transcriptome of the all g-treated spaceflight samples was compared with microgravity samples, only ~130 genes were identified as being differently regulated (P ≤ 0.01). Of this subset, only 27 genes were at least twofold differently regulated between microgravity and 1g space samples and included putative/pseudo/undefined genes (14), transposable elements (5), an expansin (ATEXP24; At1g21240), a cell-wall kinase (WAK3; At1g21240), a laccase-like flavonoid oxidase (TT10; At5g48100), among others.

MIZ1-regulated hydrotropism functions in the growth and survival of Arabidopsis thaliana under natural conditions

BACKGROUND AND AIMS

Root hydrotropism is a response to water-potential gradients that makes roots bend towards areas of higher water potential. The gene MIZU-KUSSEI1 (MIZ1) that is essential for hydrotropism in Arabidopsis roots has previously been identified. However, the role of root hydrotropism in plant growth and survival under natural conditions has not yet been proven. This study assessed how hydrotropic response contributes to drought avoidance in nature.

METHODS

An experimental system was established for the study of Arabidopsis hydrotropism in soil. Characteristics of hydrotropism were analysed by comparing the responses of the miz1 mutant, transgenic plants overexpressing MIZ1 (MIZ1OE) and wild-type plants.

KEY RESULTS

Wild-type plants developed root systems in regions with higher water potential, whereas the roots of miz1 mutant plants did not show a similar response. This pattern of root distribution induced by hydrotropism was more pronounced in MIZ1OE plants than in wild-type plants. In addition, shoot biomass and the number of plants that survived under drought conditions were much greater in MIZ1OE plants.

CONCLUSIONS

These results show that hydrotropism plays an important role in root system development in soil and contributes to drought avoidance, which results in a greater yield and plant survival under water-limited conditions. The results also show that MIZ1 overexpression can be used for improving plant productivity in arid areas.