Far-Red Light Detection in the Shoot Regulates Lateral Root Development through the HY5 Transcription Factor

Effect of Low Red-to-Far-Red Light on Stem Elongation and Pith Cell Development in Dicots

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.

Expression variation of Viola APETALA3 orthologous genes is correlated with chasmogamous and cleistogamous flower development

BACKGROUND

Viola philippica and V. prionantha develop chasmogamous (CH) flowers under ≤ 12-h daylight conditions and cleistogamous (CL) flowers under long daylight (> 12-h daylight) conditions (LD), whereas V. cornuta develops CH flowers regardless of the daylight conditions. APETALA3 (AP3) is a major floral B-function gene that regulates the organ identity and development of stamens and petals. Evolutionary changes in AP3 orthologous genes might involve in the dimorphic flower formation. In the present study, we compared AP3 orthologous genes among three Viola species.

RESULTS

The AP3 sequences were highly conserved, and obligate AP3-PISTILLATA heterodimers were universally formed. However, the floral expression of VphAP3 in V. philippica and VprAP3 in V. prionantha changed in response to the photoperiod. Their expression was significantly higher under 12-h daylight conditions than under 16-h daylight conditions. In contrast, VcoAP3 expression in the floral buds of V. cornuta was comparable among photoperiods. In accordance with these variations in expression, correlated sequence divergences were observed in the putative regulatory regions of Viola AP3 orthologous genes.

CONCLUSIONS

Developmental inhibition of petals and stamens may result from AP3 downregulation by LD, which thereby induces CL flowers. Our study provides insight into the molecular basis underlying the developmental evolution of environmentally dependent mating systems in dimorphic CL plants.

ELONGATED HYPOCOTYL 5 promotes root growth by maintaining redox homeostasis and repressing oxidative stress response

Oxidative stress is a major threat to plant growth and survival. To understand how plants cope with oxidative stress, we carried out a genetic screen for Arabidopsis (Arabidopsis thaliana) mutants with altered response to hydrogen peroxide (H2O2) in root growth. Herein, we report the characterization of one of the hypersensitive mutants obtained. This mutant had slightly shorter roots in normal growth medium, and this phenotype became more pronounced in H2O2-containing medium. Through genome-wide resequencing and complementation experiments, we identified the gene with the causal mutation as ELONGATED HYPOCOTYL 5 (HY5). Histochemical staining revealed that the apical meristem of hy5 roots had an elevated level of H2O2 but a lower level of superoxide. In further experiments, we showed that genes involved in redox homeostasis and oxidative response were altered in hy5 roots and that MYB DOMAIN PROTEIN 30 (MYB30), GLUTATHIONE S-TRANSFERASE PHI 2 (GSTF2), and GLUTATHIONE S-TRANSFERASE TAU 19 (GSTU19) are directly repressed by HY5. Interestingly, overexpression of MYB30, a master regulator of the oxidative stress response, exacerbated the root growth defect in hy5, whereas knocking it down by RNAi largely rescued the mutant's hypersensitivity to H2O2 without affecting the content of reactive oxygen species (ROS). Intriguingly, knocking down GSTF2 also rescued the H2O2 hypersensitivity and ROS homeostasis defects in hy5 roots. In addition to H2O2, we showed that hy5 was also hypersensitive to high salinity, Cd, and salicylic acid. Based on these results, we conclude that HY5 plays a positive role in root growth mainly under abiotic stress by modulating both redox homeostasis and oxidative stress response.

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

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

Cycling Dof Factor 3 mediates light-dependent ascorbate biosynthesis by activating GDP-l-galactose phosphorylase in Rosa roxburghii fruit

Light plays an important role in determining the l-ascorbate (AsA) pool size in plants, primarily through the transcriptional regulation of AsA metabolism-related genes. However, the specific mechanism of transcriptional induction responsible for light-dependent AsA biosynthesis remains unclear. In this study, we used a promoter sequence containing light-responsive motifs from GDP-L-galactose phosphorylase 2 (RrGGP2), a key gene involved in AsA overproduction in Rosa roxburghii fruits, to identify participating transcription factors. Among these factors, Cycling Dof Factor 3 (RrCDF3) was highly responsive to variations in light intensity, quality, and photoperiod, leading to alterations in RrGGP2 expression. Further yeast one-hybrid and dual-luciferase assays confirmed that RrCDF3 acts as a transcriptional activator of RrGGP2 by binding specifically to its promoter. Modulating the expression of RrCDF3 in fruits through transient overexpression and silencing resulted in significant changes in RrGGP2 expression and AsA synthesis. Additionally, the stable overexpression of RrCDF3 in R. roxburghii calli and Solanum lycopersicum plants resulted in a significant increase in AsA content. Notably, the well-known photo-signal transcription factor ELONGATED HYPOCOTYL5 (RrHY5) directly interacted with the RrCDF3 promoter, enhancing its transcription. These findings reveal a special mechanism involving the RrHY5-RrCDF3-RrGGP2 module that mediates light-induced AsA biosynthesis in R. roxburghii fruit.

Spatiotemporal bifurcation of HY5-mediated blue-light signaling regulates wood development during secondary growth

Plants have evolved photoreceptors to optimize their development during primary growth, including germination, hypocotyl elongation, cotyledon opening, and root growth, allowing them to adapt to challenging light conditions. The light signaling transduction pathway during seedling establishment has been extensively studied, but little molecular evidence is available for light-regulated secondary growth, and how light regulates cambium-derived tissue production remains largely unexplored. Here, we show that CRYPTOCHROME (CRY)-dependent blue light signaling and the subsequent attenuation of ELONGATED HYPOCOTYL 5 (HY5) movement to hypocotyls are key inducers of xylem fiber differentiation in Arabidopsis thaliana. Using grafted chimeric plants and hypocotyl-specific transcriptome sequencing of light signaling mutants under controlled light conditions, we demonstrate that the perception of blue light by CRYs in shoots drives secondary cell wall (SCW) deposition at xylem fiber cells during the secondary growth of hypocotyls. We propose that HY5 is a blue light-responsive mobile protein that inhibits xylem fiber formation via direct transcriptional repression of NAC SECONDARY WALL THICKENING PROMOTING 3 (NST3). CRYs retain HY5 in the nucleus, impede its long-distance transport from leaf to hypocotyl, and they initiate NST3-driven SCW gene expression, thereby triggering xylem fiber production. Our findings shed light on the long-range CRYs-HY5-NST3 signaling cascade that shapes xylem fiber development, highlighting the activity of HY5 as a transcriptional repressor during secondary growth.

ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana

Injured plant somatic tissues regenerate themselves by establishing shoot or root meristems. In Arabidopsis (Arabidopsis thaliana), a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, whether and how environmental factors influence this process remains elusive. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyls as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristems through the regulatory network governed by HY5, thus highlighting the influence of light signals on plant developmental plasticity.

Temporal and spatial frameworks supporting plant responses to vegetation proximity

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

RACK1 links phyB and BES1 to coordinate brassinosteroid-dependent root meristem development

Light and brassinosteroids (BR) are indispensable for plant growth and control cell division in the apical meristem. However, how external light signals cooperate with internal brassinosteroids to program root meristem development remains elusive. We reveal that the photoreceptor phytochrome B (phyB) guides the scaffold protein RACK1 to coordinate BR signaling for maintaining root meristematic activity. phyB and RACK1 promote early root meristem development. Mechanistically, RACK1 could reinforce the phyB-SPA1 association by interacting with both phyB and SPA1, which indirectly affects COP1-dependent RACK1 degradation, resulting in the accumulation of RACK1 in roots. Subsequently, RACK1 interacts with BES1 to repress its DNA-binding activity toward the target gene CYCD3;1, leading to the release of BES1-mediated inhibition of CYCD3;1 transcription, and hence the promotion of root meristem development. Our study provides mechanistic insights into the regulation of root meristem development by combination of light and phytohormones signals through the photoreceptors and scaffold proteins.

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 investigated how Arabidopsis integrates shade and nitrate signalling. We unveiled that nitrate modulates shade avoidance via a previously unknown shade response pathway that involves root-derived trans-zeatin (tZ) signal and the BEE1 transcription factor as an integrator of light and cytokinin signalling. Under nitrate-sufficient conditions, tZ promotes hypocotyl elongation specifically in the presence of supplemental far-red light. This occurs via PIF transcription factors-dependent inhibition of type-A ARRs cytokinin response inhibitors. Our data thus reveal how plants co-regulate responses to shade cues with root-derived information about nutrient availability, and how they restrict responses to this information to specific light conditions in the shoot.

Recent advances in local and systemic nitrate signaling in Arabidopsisthaliana

Nitrate is the most abundant form of inorganic nitrogen in aerobic soils, serving both as a nutrient and a signaling molecule. Central to nitrate signaling in higher plants is the intricate balance between local and systemic signaling and response pathways. The interplay between local and systemic responses allows plants to regulate their global gene expression, metabolism, physiology, growth, and development under fluctuating nitrate availability. This review offers an overview of recent discoveries regarding new players on nitrate sensing and signaling, in local and systemic contexts in Arabidopsis thaliana. Additionally, it addresses unanswered questions that warrant further investigation for a better understanding of nitrate signaling and responses in plants.

Recent advances in response to environmental signals during Arabidopsis root development

Plants grow by anchoring their roots in the soil, acquiring essential water and nutrients for growth, and interacting with other signaling factors in the soil. Root systems are crucial for both the basic growth and development of plants and their response to external environmental stimuli. Under different environmental conditions, the configuration of root systems in plants can undergo significant changes, with their strength determining the plant's ability to adapt to the environment. Therefore, understanding the mechanisms by which environmental factors regulate root development is essential for crop root architecture improvement and breeding for stress resistance. This paper summarizes the research progress in genetic regulation of root development of the model plant Arabidopsis thaliana (L.) Heynh. amidst diverse environmental stimuli over the past five years. Specifically, it focuses on the regulatory networks of environmental signals, encompassing light, energy, temperature, water, nutrients, and reactive oxygen species, on root development. Furthermore, it provides prospects for the application of root architecture improvement in crop breeding for stress resistance and nutrient efficiency.

Meta-Analysis of the Impact of Far-Red Light on Vegetable Crop Growth and Quality

Far-red lights (FRs), with a wavelength range between 700 and 800 nm, have substantial impacts on plant growth, especially horticultural crops. Previous studies showed conflicting results on the effects of FRs on vegetable growth and quality. Therefore, we conducted a meta-analysis on the influence of FRs on vegetable growth, aiming to provide a comprehensive overview of their effects on the growth and nutritional indicators of vegetables. A total of 207 independent studies from 55 literature sources were analyzed. The results showed that FR treatment had significant effects on most growth indicators, including increasing the fresh weight (+25.27%), dry weight (+21.99%), plant height (+81.87%), stem diameter (+12.91%), leaf area (+18.57%), as well as reducing the content of chlorophyll (-11.88%) and soluble protein (-11.66%), while increasing soluble sugar content (+19.12%). Further subgroup analysis based on various factors revealed significant differences in the effects of FR on different physiological indicators, such as FR intensity, plant species, duration of FR exposure, and the ratio of red light to FR. In general, moderate FR treatment is beneficial for vegetable growth. This study provides important references and guidelines for optimizing the application of FR in the future.

HY5 and PIF antagonistically regulate HMGR expression and sterol biosynthesis in Arabidopsis thaliana

Secondary metabolites play multiple crucial roles in plants by modulating various regulatory networks. The biosynthesis of these compounds is unique to each species and is intricately controlled by a range of developmental and environmental factors. While light's role in certain secondary metabolites is evident, its impact on sterol biosynthesis remains unclear. Previous studies indicate that ELONGATED HYPOCOTYL5 (HY5), a bZIP transcription factor, is pivotal in skotomorphogenesis to photomorphogenesis transition. Additionally, PHYTOCHROME INTERACTING FACTORs (PIFs), bHLH transcription factors, act as negative regulators. To unveil the light-dependent regulation of the mevalonic acid (MVA) pathway, a precursor for sterol biosynthesis, mutants of light signaling components, specifically hy5-215 and the pifq quadruple mutant (pif 1,3,4, and 5), were analyzed in Arabidopsis thaliana. Gene expression analysis in wild-type and mutants implicates HY5 and PIFs in regulating sterol biosynthesis genes. DNA-protein interaction analysis confirms their interaction with key genes like AtHMGR2 in the rate-limiting pathway. Results strongly suggest HY5 and PIFs' pivotal role in light-dependent MVA pathway regulation, including the sterol biosynthetic branch, in Arabidopsis, highlighting a diverse array of light signaling components finely tuning crucial growth pathways.

Light at the end of the tunnel: integrating signaling pathways in the coordination of lateral root development

Root system architecture (RSA) encompasses a range of physical root attributes, including the lateral roots (LRs), root hairs and adventitious roots, in addition to the primary or main root. This overall structure is a crucial trait for efficient water and mineral capture alongside providing anchorage to the plant in the soil and is vital for plant productivity and fitness. RSA dynamics are dependent upon various environmental cues such as light, soil pH, water, mineral nutrition and the belowground microbiome. Among these factors, light signaling through HY5 significantly influences the flexibility of RSA by controlling different signaling pathways that converge at photoreceptors-mediated signaling, also present in the 'hidden half'. Furthermore, several phytohormones also drive the formation and emergence of LRs and are critical to harmonize intra and extracellular stimuli in this regard. This review endeavors to elucidate the impact of these interactions on RSA, with particular emphasis on LR development and to enhance our understanding of the fundamental mechanisms governing the light-regulation of LR growth and physiology.

A Highly Efficient Agrobacterium rhizogenes-Mediated Hairy Root Transformation Method of Idesia polycarpa and the Generation of Transgenic Plants

Idesia polycarpa is a promising woody oilseed species because of its high oil yield. However, its use is greatly limited due to the lack of varieties with good qualities; additionally, gene function has been less studied in this plant because an efficient transformation method has not been established yet. In this study, we established a rapid and efficient hairy root transformation method by infecting the whole seedling, the rootless seedling, and the leaf petiole with Agrobacterium rhizogenes using different infection methods. Among these transformation methods, a higher transformation efficiency was obtained using the whole seedling, which could reach up to 71.91%. Furthermore, we found that the seedling age significantly affected the transformation efficiency, either using whole or rootless seedlings. Additionally, we found that the transgenic roots could regenerate transgenic shoots. Taken together, our study lays the foundation for future study and for genetically modifying wood traits in the future.

Regulation of stomatal development by epidermal, subepidermal and long-distance signals

Plant leaves consist of three layers, including epidermis, mesophyll and vascular tissues. Their development is meticulously orchestrated. Stomata are the specified structures on the epidermis for uptake of carbon dioxide (CO2) while release of water vapour and oxygen (O2), and thus play essential roles in regulation of plant photosynthesis and water use efficiency. To function efficiently, stomatal formation must coordinate with the development of other epidermal cell types, such as pavement cell and trichome, and tissues of other layers, such as mesophyll and leaf vein. This review summarizes the regulation of stomatal development in three dimensions (3D). In the epidermis, specific stomatal transcription factors determine cell fate transitions and also activate a ligand-receptor- MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) signaling for ensuring proper stomatal density and patterning. This forms the core regulation network of stomatal development, which integrates various environmental cues and phytohormone signals to modulate stomatal production. Under the epidermis, mesophyll, endodermis of hypocotyl and inflorescence stem, and veins in grasses secrete mobile signals to influence stomatal formation in the epidermis. In addition, long-distance signals which may include phytohormones, RNAs, peptides and proteins originated from other plant organs modulate stomatal development, enabling plants to systematically adapt to the ever changing environment.

Effect of red and blue light versus white light on fruit biomass radiation-use efficiency in dwarf tomatoes

The effect of the ratio of red and blue light on fruit biomass radiation-use efficiency (FBRUE) in dwarf tomatoes has not been well studied. Additionally, whether white light offers a greater advantage in improving radiation-use efficiency (RUE) and FBRUE over red and blue light under LED light remains unknown. In this study, two dwarf tomato cultivars ('Micro-Tom' and 'Rejina') were cultivated in three red-blue light treatments (monochromatic red light, red/blue light ratio = 9, and red/blue light ratio = 3) and a white light treatment at the same photosynthetic photon flux density of 300 μmol m-2 s-1. The results evidently demonstrated that the red and blue light had an effect on FBRUE by affecting RUE rather than the fraction of dry mass partitioned into fruits (Ffruits). The monochromatic red light increased specific leaf area, reflectance, and transmittance of leaves but decreased the absorptance and photosynthetic rate, ultimately resulting in the lowest RUE, which induced the lowest FBRUE among all treatments. A higher proportion of blue light (up to 25%) led to a higher photosynthetic rate, resulting in a higher RUE and FBRUE in the three red-blue light treatments. Compared with red and blue light, white light increased RUE by 0.09-0.38 g mol-1 and FBRUE by 0.14-0.25 g mol-1. Moreover, white light improved the Ffruits in 'Rejina' and Brix of fruits in 'Micro-Tom' and both effects were cultivar-specific. In conclusion, white light may have greater potential than mixed red and blue light for enhancing the dwarf tomato FBRUE during their reproductive growth stage.

PHYTOCHROME A controls the DNA damage response and cell death tolerance within the Arabidopsis root meristem

The DNA damage response avoids mutations into dividing cells. Here, we analysed the role of photoreceptors on the restriction of root growth imposed by genotoxic agents and its relationship with cell viability and performance of meristems. Comparison of root growth of Arabidopsis WT, phyA-211, phyB-9, and phyA-211phyB-9 double mutants unveiled a critical role for phytochrome A (PhyA) in protecting roots from genotoxic stress, regeneration and cell replenishment in the meristematic zone. PhyA was located on primary root tips, where it influences genes related to the repair of DNA, including ERF115 and RAD51. Interestingly, phyA-211 mutants treated with zeocin failed to induce the expression of the repressor of cell cycle MYB3R3, which correlated with expression of the mitotic cyclin CycB1, suggesting that PhyA is required for safeguarding the DNA integrity during cell division. Moreover, the growth of the primary roots of PhyA downstream component HY5 and root growth analyses in darkness suggest that cell viability and DNA damage responses within root meristems may act independently from light and photomorphogenesis. These data support novel roles for PhyA as a key player for stem cell niche maintenance and DNA damage responses, which are critical for proper root growth.

ELONGATED HYPOTCOTYL5 and SPINE BASE SIZE1 together mediate light-regulated spine expansion in cucumber

Plant trichome development is influenced by diverse developmental and environmental signals, but the molecular mechanisms involved are not well understood in most plant species. Fruit spines (trichomes) are an important trait in cucumber (Cucumis sativus L.), as they affect both fruit smoothness and commercial quality. Spine Base Size1 (CsSBS1) has been identified as essential for regulating fruit spine size in cucumber. Here, we discovered that CsSBS1 controls a season-dependent phenotype of spine base size in wild-type plants. Decreased light intensity led to reduced expression of CsSBS1 and smaller spine base size in wild-type plants, but not in the mutants with CsSBS1 deletion. Additionally, knockout of CsSBS1 resulted in smaller fruit spine base size and eliminated the light-induced expansion of spines. Overexpression of CsSBS1 increased spine base size and rescued the decrease in spine base size under low light conditions. Further analysis revealed that ELONGATED HYPOTCOTYL5 (HY5), a major transcription factor involved in light signaling pathways, directly binds to the promoter of CsSBS1 and activates its expression. Knockout of CsHY5 led to smaller fruit spine base size and abolished the light-induced expansion of spines. Taken together, our study findings have clarified a CsHY5-CsSBS1 regulatory module that mediates light-regulated spine expansion in cucumber. This finding offers a strategy for cucumber breeders to develop fruit with stable appearance quality under changing light conditions.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Strong prevalence of light regime-specific QTL in Arabidopsis detected using automated high-throughput phenotyping in fluctuating or constant light

Plants have evolved and adapted under dynamic environmental conditions, particularly to fluctuating light, but plant research has often focused on constant growth conditions. To quantitatively asses the adaptation to fluctuating light, a panel of 384 natural Arabidopsis thaliana accessions was analyzed in two parallel independent experiments under fluctuating and constant light conditions in an automated high-throughput phenotyping system upgraded with supplemental LEDs. While the integrated daily photosynthetically active radiation was the same under both light regimes, plants in fluctuating light conditions accumulated significantly less biomass and had lower leaf area during their measured vegetative growth than plants in constant light. A total of 282 image-derived architectural and/or color-related traits at six common time points, and 77 photosynthesis-related traits from one common time point were used to assess their associations with genome-wide natural variation for both light regimes. Out of the 3000 significant marker-trait associations (MTAs) detected, only 183 (6.1%) were common for fluctuating and constant light conditions. The prevalence of light regime-specific QTL indicates a complex adaptation. Genes in linkage disequilibrium with fluctuating light-specific MTAs with an adjusted repeatability value >0.5 were filtered for gene ontology terms containing "photo" or "light", yielding 15 selected candidates. The candidate genes are involved in photoprotection, PSII maintenance and repair, maintenance of linear electron flow, photorespiration, phytochrome signaling, and cell wall expansion, providing a promising starting point for further investigations into the response of Arabidopsis thaliana to fluctuating light conditions.

"Genome-wide identification of bZIP gene family in Pearl millet and transcriptional profiling under abiotic stress, phytohormonal treatments; and functional characterization of PgbZIP9"

Abiotic stresses are major constraints in crop production, and are accountable for more than half of the total crop loss. Plants overcome these environmental stresses using coordinated activities of transcription factors and phytohormones. Pearl millet an important C4 cereal plant having high nutritional value and climate resilient features is grown in marginal lands of Africa and South-East Asia including India. Among several transcription factors, the basic leucine zipper (bZIP) is an important TF family associated with diverse biological functions in plants. In this study, we have identified 98 bZIP family members (PgbZIP) in pearl millet. Phylogenetic analysis divided these PgbZIP genes into twelve groups (A-I, S, U and X). Motif analysis has shown that all the PgbZIP proteins possess conserved bZIP domains and the exon-intron organization revealed conserved structural features among the identified genes. Cis-element analysis, RNA-seq data analysis, and real-time expression analysis of PgbZIP genes suggested the potential role of selected PgbZIP genes in growth/development and abiotic stress responses in pearl millet. Expression profiling of selected PgbZIPs under various phytohormones (ABA, SA and MeJA) treatment showed differential expression patterns of PgbZIP genes. Further, PgbZIP9, a homolog of AtABI5 was found to localize in the nucleus and modulate gene expression in pearl millet under stresses. Our present findings provide a better understanding of bZIP genes in pearl millet and lay a good foundation for the further functional characterization of multi-stress tolerant PgbZIP genes, which could become efficient tools for crop improvement.

Above and belowground phenotypic response to exogenous auxin across Arabidopsis thaliana mutants and natural accessions varies from seedling to reproductive maturity

Background

Plant hormones influence phenology, development, and function of above and belowground plant structures. In seedlings, auxin influences the initiation and development of lateral roots and root systems. How auxin-related genes influence root initiation at early life stages has been investigated from numerous perspectives. There is a gap in our understanding of how these genes influence root size through the life cycle and in mature plants. Across development, the influence of a particular gene on plant phenotypes is partly regulated by the addition of a poly-A tail to mRNA transcripts via alternative polyadenylation (APA). Auxin related genes have documented variation in APA, with auxin itself contributing to APA site switches. Studies of the influence of exogenous auxin on natural plant accessions and mutants of auxin pathway gene families exhibiting variation in APA are required for a more complete understanding of genotype by development by hormone interactions in whole plant and fitness traits.

Methods

We studied Arabidopsis thaliana homozygous mutant lines with inserts in auxin-related genes previously identified to exhibit variation in number of APA sites. Our growth chamber experiment included wildtype Col-0 controls, mutant lines, and natural accession phytometers. We applied exogenous auxin through the life cycle. We quantified belowground and aboveground phenotypes in 14 day old, 21 day old seedlings and plants at reproductive maturity. We contrasted root, rosette and flowering phenotypes across wildtype, auxin mutant, and natural accession lines, APA groups, hormone treatments, and life stages using general linear models.

Results

The root systems and rosettes of mutant lines in auxin related genes varied in response to auxin applications across life stages and varied between genotypes within life stages. In seedlings, exposure to auxin decreased size, but increased lateral root density, whereas at reproductive maturity, plants displayed greater aboveground mass and total root length. These differences may in part be due to a shift which delayed the reproductive stage when plants were treated with auxin. Root traits of auxin related mutants depended on the number of APA sites of mutant genes and the plant's developmental stage. Mutants with inserts in genes with many APA sites exhibited lower early seedling belowground biomass than those with few APA sites but only when exposed to exogenous auxin. As we observed different responses to exogenous auxin across the life cycle, we advocate for further studies of belowground traits and hormones at reproductive maturity. Studying phenotypic variation of genotypes across life stages and hormone environments will uncover additional shared patterns across traits, assisting efforts to potentially reach breeding targets and enhance our understanding of variation of genotypes in natural systems.

Root-specific photoreception directs early root development by HY5-regulated ROS balance

Root development is tightly controlled by light, and the response is thought to depend on signal transmission from the shoot. Here, we show that the root apical meristem perceives light independently from aboveground organs to activate the light-regulated transcription factor ELONGATED HYPOCOTYL5 (HY5). The ROS balance between H2O2 and superoxide anion in the root is disturbed under darkness with increased H2O2. We demonstrate that root-derived HY5 directly activates PER6 expression to eliminate H2O2. Moreover, HY5 directly represses UPBEAT1, a known inhibitor of peroxidases, to release the expression of PERs, partially contributing to the light control of ROS balance in the root. Our results reveal an unexpected ability in roots with specific photoreception and provide a mechanistic framework for the HY5-mediated interaction between light and ROS signaling in early root development.

Cloned genes and genetic regulation of anthocyanin biosynthesis in maize, a comparative review

Anthocyanins are plant-based pigments that are primarily present in berries, grapes, purple yam, purple corn and black rice. The research on fruit corn with a high anthocyanin content is not sufficiently extensive. Considering its crucial role in nutrition and health it is vital to conduct further studies on how anthocyanin accumulates in fruit corn and to explore its potential for edible and medicinal purposes. Anthocyanin biosynthesis plays an important role in maize stems (corn). Several beneficial compounds, particularly cyanidin-3-O-glucoside, perlagonidin-3-O-glucoside, peonidin 3-O-glucoside, and their malonylated derivatives have been identified. C1, C2, Pl1, Pl2, Sh2, ZmCOP1 and ZmHY5 harbored functional alleles that played a role in the biosynthesis of anthocyanins in maize. The Sh2 gene in maize regulates sugar-to-starch conversion, thereby influencing kernel quality and nutritional content. ZmCOP1 and ZmHY5 are key regulatory genes in maize that control light responses and photomorphogenesis. This review concludes the molecular identification of all the genes encoding structural enzymes of the anthocyanin pathway in maize by describing the cloning and characterization of these genes. Our study presents important new understandings of the molecular processes behind the manufacture of anthocyanins in maize, which will contribute to the development of genetically modified variants of the crop with increased color and possible health advantages.

A low red/far-red ratio restricts nitrogen assimilation by inhibiting nitrate reductase associated with downregulated TaNR1.2 and upregulated TaPIL5 in wheat (Triticum aestivum L.)

Understanding the physiological mechanism underlying nitrogen levels response to a low red/far-red ratio (R/FR) can provide new insights for optimizing wheat yield potential but has been not well documented. This study focused on the changes in nitrogen levels, nitrogen assimilation and nitrate uptake in wheat plants grown with and without additional far-red light. A low R/FR reduced wheat nitrogen accumulation and grain yield compared with the control. The levels of total nitrogen, free amino acid and ammonium were decreased in leaves but nitrate content was temporarily increased under a low R/FR. The nitrate reductase (NR) activity in leaves was more sensitive to a low R/FR than glutamine synthetase, glutamate synthase, glutamic oxalacetic transaminase and glutamic-pyruvic transaminase. Further analysis showed that a low R/FR had little effect on the NR activation state but reduced the level of NR protein and the expression of encoding gene TaNR1.2. Interestingly, a low R/FR rapidly induced TaPIL5 expression rather than TaHY5 and other members of TaPILs in wheat, suggesting that TaPIL5 was the key transcription factor response to a low R/FR in wheat and might be involved in the downregulation of TaNR1.2 expression. Besides, a low R/FR downregulated the expression of TaNR1.2 in leaves earlier than that of TaNRT1.1/1.2/1.5/1.8 in roots, which highlights the importance of NR and nitrogen assimilation in response to a low R/FR. Our results provide revelatory evidence that restricted nitrate reductase associated with downregulated TaNR1.2 and upregulated TaPIL5 mediate the suppression of nitrogen assimilation under a low R/FR in wheat.

Genetic regulation of lateral root development

Lateral roots (LRs) are an important part of plant root systems. In dicots, for example, after plants adapted from aquatic to terrestrial environments, filamentous pseudorhizae evolved to allow nutrient absorption. A typical plant root system comprises a primary root, LRs, root hairs, and a root cap. Classical plant roots exhibit geotropism (the tendency to grow downward into the ground) and can synthesize plant hormones and other essential substances. Root vascular bundles and complex spatial structures enable plants to absorb water and nutrients to meet their nutrient quotas and grow. The primary root carries out most functions during early growth stages but is later overtaken by LRs, underscoring the importance of LR development water and mineral uptake and the soil fixation capacity of the root. LR development is modulated by endogenous plant hormones and external environmental factors, and its underlying mechanisms have been dissected in great detail in Arabidopsis, thanks to its simple root anatomy and the ease of obtaining mutants. This review comprehensively and systematically summarizes past research (largely in Arabidopsis) on LR basic structure, development stages, and molecular mechanisms regulated by different factors, as well as future prospects in LR research, to provide broad background knowledge for root researchers.

Illuminating the path to shoot meristem regeneration: Molecular insights into reprogramming cells into stem cells

Plant cells possess the ability to dedifferentiate and reprogram into stem cell-like populations, enabling the regeneration of new organs. However, the maintenance of stem cells relies on specialized microenvironments composed of distinct cell populations with specific functions. Consequently, the regeneration process necessitates the orchestrated regulation of multiple pathways across diverse cellular populations. One crucial pathway involves the transcription factor WUSCHEL HOMEOBOX 5 (WOX5), which plays a pivotal role in reprogramming cells into stem cells and promoting their conversion into shoot meristems through WUSCHEL (WUS). Additionally, cell and tissue mechanics, including cell wall modifications and mechanical stress, critically contribute to de novo shoot organogenesis by regulating polar auxin transport. Furthermore, light signaling emerges as a key regulator of plant regeneration, directly influencing expression of meristem genes and potentially influencing aforementioned pathways as well.

Functions of sucrose and trehalose 6-phosphate in controlling plant development

Plants exhibit enormous plasticity in regulating their architecture to be able to adapt to a constantly changing environment and carry out vital functions such as photosynthesis, anchoring, and nutrient uptake. Phytohormones play a role in regulating these responses, but sugar signalling mechanisms are also crucial. Sucrose is not only an important source of carbon and energy fuelling plant growth, but it also functions as a signalling molecule that influences various developmental processes. Trehalose 6-phosphate (Tre6P), a sucrose-specific signalling metabolite, is emerging as an important regulator in plant metabolism and development. Key players involved in sucrose and Tre6P signalling pathways, including MAX2, SnRK1, bZIP11, and TOR, have been implicated in processes such as flowering, branching, and root growth. We will summarize our current knowledge of how these pathways shape shoot and root architecture and highlight how sucrose and Tre6P signalling are integrated with known signalling networks in shaping plant growth.

Tunable recurrent priming of lateral roots in Arabidopsis: More than just a clock?

Lateral root (LR) formation in Arabidopsis is a continuous, repetitive, post-embryonic process regulated by a series of coordinated events and tuned by the environment. It shapes the root system, enabling plants to efficiently explore soil resources and adapt to changing environmental conditions. Although the auxin-regulated modules responsible for LR morphogenesis and emergence are well documented, less is known about the initial priming. Priming is characterised by recurring peaks of auxin signalling, which, once memorised, earmark cells to form the new LR. We review the recent experimental and modelling approaches to understand the molecular processes underlying the recurring LR formation. We argue that the intermittent priming of LR results from interweaving the pattern of auxin flow and root growth together with an oscillatory auxin-modulated transcriptional mechanism and illustrate its long-range sugar-mediated tuning by light.

Synergism of vesicle trafficking and cytoskeleton during regulation of plant growth and development: A mechanistic outlook

The cytoskeleton is a fundamental component found in all eukaryotic organisms, serving as a critical factor in various essential cyto-biological mechanisms, particularly in the locomotion and morphological transformations of plant cells. The cytoskeleton is comprised of three main components: microtubules (MT), microfilaments (MF), and intermediate filaments (IF). The cytoskeleton plays a crucial role in the process of cell wall formation and remodeling throughout the growth and development of cells. It is a highly organized and regulated network composed of filamentous components. In the basic processes of intracellular transport, such as mitosis, cytokinesis, and cell polarity, the plant cytoskeleton plays a crucial role according to recent studies. The major flaws in the organization of the cytoskeletal framework are at the root of the aberrant organogenesis currently observed in plant mutants. The regulation of protein compartmentalization and abundance within cells is predominantly governed by the process of vesicle/membrane transport, which plays a crucial role in several signaling cascades.The regulation of membrane transport in eukaryotic cells is governed by a diverse array of proteins. Recent developments in genomics have provided new tools to study the evolutionary relationships between membrane proteins in different plant species. It is known that members of the GTPases, COP, SNAREs, Rabs, tethering factors, and PIN families play essential roles in vesicle transport between plant, animal, and microbial species. This Review presents the latest research on the plant cytoskeleton, focusing on recent developments related to the cytoskeleton and summarizing the role of various proteins in vesicle transport. In addition, the report predicts future research direction of plant cytoskeleton and vesicle trafficking, potential research priorities, and provides researchers with specific pointers to further investigate the significant link between cytoskeleton and vesicle trafficking.

Does day length matter for nutrient responsiveness?

For over 2500 years, considerable agronomic interest has been paid to soil fertility. Both crop domestication and the Green Revolution shifted photoperiodism and the circadian clock in cultivated species, although this contributed to an increase in the demand for chemical fertilisers. Thus, the uptake of nutrients depends on light signalling, whereas diel growth and circadian rhythms are affected by nutrient levels. Here, we argue that day length and circadian rhythms may be central regulators of the uptake and usage of nutrients, also modulating responses to toxic elements (e.g., aluminium and cadmium). Thus, we suggest that knowledge in this area might assist in developing next-generation crops with improved uptake and use efficiency of nutrients.

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

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

Two splice forms of OsbZIP1, a homolog of AtHY5, function to regulate skotomorphogenesis and photomorphogenesis in rice

Plants possess well-developed light sensing mechanisms and signal transduction systems for regulating photomorphogenesis. ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) transcription factor, has been extensively characterized in dicots. In this study, we show that OsbZIP1 is a functional homolog of Arabidopsis (Arabidopsis thaliana) HY5 (AtHY5) and is important for light-mediated regulation of seedling and mature plant development in rice (Oryza sativa). Ectopic expression of OsbZIP1 in rice reduced plant height and leaf length without affecting plant fertility, which contrasts with OsbZIP48, a previously characterized HY5 homolog. OsbZIP1 is alternatively spliced, and the OsbZIP1.2 isoform lacking the CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)-binding domain regulated seedling development in the dark. Rice seedlings overexpressing OsbZIP1 were shorter than the vector control under white and monochromatic light conditions, whereas RNAi knockdown seedlings displayed the opposite phenotype. While OsbZIP1.1 was light-regulated, OsbZIP1.2 showed a similar expression profile in both light and dark conditions. Due to its interaction with OsCOP1, OsbZIP1.1 undergoes 26S proteasome-mediated degradation under dark conditions. Also, OsbZIP1.1 interacted with and was phosphorylated by CASEIN KINASE2 (OsCK2α3). In contrast, OsbZIP1.2 did not show any interaction with OsCOP1 or OsCK2α3. We propose that OsbZIP1.1 likely regulates seedling development in the light, while OsbZIP1.2 is the dominant player under dark conditions. The data presented in this study reveal that AtHY5 homologs in rice have undergone neofunctionalization, and alternative splicing of OsbZIP1 has increased the repertoire of its functions.

The Role of Light Quality in Regulating Early Seedling Development

It is well-established that plants are sessile and photoautotrophic organisms that rely on light throughout their entire life cycle. Light quality (spectral composition) is especially important as it provides energy for photosynthesis and influences signaling pathways that regulate plant development in the complex process of photomorphogenesis. During previous years, significant progress has been made in light quality's physiological and biochemical effects on crops. However, understanding how light quality modulates plant growth and development remains a complex challenge. In this review, we provide an overview of the role of light quality in regulating the early development of plants, encompassing processes such as seed germination, seedling de-etiolation, and seedling establishment. These insights can be harnessed to improve production planning and crop quality by producing high-quality seedlings in plant factories and improving the theoretical framework for modern agriculture.

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

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

Effect of Low Light Stress on Distribution of Auxin (Indole-3-acetic Acid) between Shoot and Roots and Development of Lateral Roots in Barley Plants

Depending on their habitat conditions, plants can greatly change the growth rate of their roots. However, the mechanisms of such responses remain insufficiently clear. The influence of a low level of illumination on the content of endogenous auxins, their localization in leaves and transport from shoots to roots were studied and related to the lateral root branching of barley plants. Following two days' reduction in illumination, a 10-fold reduction in the emergence of lateral roots was found. Auxin (IAA, indole-3-acetic acid) content decreased by 84% in roots and by 30% in shoots, and immunolocalization revealed lowered IAA levels in phloem cells of leaf sections. The reduced content of IAA found in the plants under low light suggests an inhibition of production of this hormone under these conditions. At the same time, two-fold downregulation of the LAX3 gene expression, facilitating IAA influx into the cells, was detected in the roots, as well as a decline in auxin diffusion from shoots through the phloem by about 60%. It was suggested that the reduced emergence of lateral roots in barley under a low level of illumination was due to a disturbance of auxin transport through the phloem and down-regulation of the genes responsible for auxin transport in plant roots. The results confirm the importance of the long distance transport of auxins for the control of the growth of roots under conditions of low light. Further study of the mechanisms that control the transport of auxins from shoots to roots in other plant species is required.

Light induced shoot-sourced transcription factor HY5 regulates the nitrate uptake of cotton by shoot-to-root signal transport

Elongated hypocotyls 5 (HY5) is a transcription factor that can be induced by illumination and promotes nitrate uptake in Arabidopsis. However, whether GhHY5 regulates nitrate uptake in cotton is unknown. In this study, the cotton seedlings growing in light and dark conditions were treated with ¹⁵N-labeled nutrient solution to study whether the GhHY5 regulates nitrate uptake in cotton. The results showed that the ¹⁵N content and GhNRT1.1 expression in the light condition were higher than that in the dark condition, indicating that light induced the expression of GhNRT1.1 and subsequently promoted N uptake. Additionally, the expression of GhHY5 in the leaf and root of cotton was induced by light and the expression pattern of GhHY5 in the root was similar to that of GhNRT1.1. Furthermore, when the GhHY5 expression in the root was reduced, the ¹⁵N content and GhNRT1.1 expression were both decreased, indicating that the GhNRT1.1 expression was regulated by GhHY5. The root expression of GhHY5 was decreased in the grafted seedlings which the GhHY5 in the shoot was silenced by VIGS or the seedlings which the hypocotyl was girdled, but the expression of GhHY5 on one side root of the grafted cotton seedling was not changed if the GhHY5 was silenced on the other side root. Thus, we proposed that the light induced shoot-derived GhHY5 gene or GhHY5 protein may be transported from the xylem to the root, regulating the expression of GhHY5 and GhNRT1.1, and thus regulating N uptake at the root of cotton.

Integration of light and ABA signaling pathways to combat drought stress in plants

Drought is one of the most critical stresses, which causes an enormous reduction in crop yield. Plants develop various strategies like drought escape, drought avoidance, and drought tolerance to cope with the reduced availability of water during drought. Plants adopt several morphological and biochemical modifications to fine-tune their water-use efficiency to alleviate drought stress. ABA accumulation and signaling plays a crucial role in the response of plants towards drought. Here, we discuss how drought-induced ABA regulates the modifications in stomatal dynamics, root system architecture, and the timing of senescence to counter drought stress. These physiological responses are also regulated by light, indicating the possibility of convergence of light- and drought-induced ABA signaling pathways. In this review, we provide an overview of investigations reporting light-ABA signaling cross talk in Arabidopsis as well as other crop species. We have also tried to describe the potential role of different light components and their respective photoreceptors and downstream factors like HY5, PIFs, BBXs, and COP1 in modulating drought stress responses. Finally, we highlight the possibilities of enhancing the plant drought resilience by fine-tuning light environment or its signaling components in the future.

HY5 inhibits lateral root initiation in Arabidopsis through negative regulation of the microtubule-stabilizing protein TPXL5

Tight control of lateral root (LR) initiation is vital for root system architecture and function. Regulation of cortical microtubule reorganization is involved in the asymmetric radial expansion of founder cells during LR initiation in Arabidopsis (Arabidopsis thaliana). However, critical genetic evidence on the role of microtubules in LR initiation is lacking and the mechanisms underlying this regulation are poorly understood. Here, we found that the previously uncharacterized microtubule-stabilizing protein TPX2-LIKE5 (TPXL5) participates in LR initiation, which is finely regulated by the transcription factor ELONGATED HYPOCOTYL5 (HY5). In tpxl5 mutants, LR density was decreased and more LR primordia (LRPs) remained in stage I, indicating delayed LR initiation. In particular, the cell width in the peripheral domain of LR founder cells after the first asymmetric cell division was larger in tpxl5 mutants than in the wild-type. Consistently, ordered transverse cortical microtubule arrays were not well generated in tpxl5 mutants. In addition, HY5 directly targeted the promoter of TPXL5 and downregulated TPXL5 expression. The hy5 mutant exhibited higher LR density and fewer stage I LRPs, indicating accelerated LR initiation. Such phenotypes were partially suppressed by TPXL5 knockout. Taken together, our data provide genetic evidence supporting the notion that cortical microtubules are essential for LR initiation and unravel a molecular mechanism underlying HY5 regulation of TPXL5-mediated microtubule reorganization and cell remodeling during LR initiation.

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.

Insights into the environmental factors shaping lateral root development

Roots are important organs of plants. Plants rely on roots for water, nutrients, and organic salts. In the whole root system, lateral roots (LRs) account for a large proportion and are critical to the development of the plant. Many environmental factors affect LR development. Therefore, a systematic understanding of these factors can provide a theoretical basis for creating optimal growth conditions for plants. In this paper, the factors affecting LR development are systematically and comprehensively summarized, and the molecular mechanism and regulatory network of LR development are described. Changes in the external environment not only lead to hormone homeostasis in plants but also affect the composition and activity of rhizosphere microbial communities, which in turn affect plants' nitrogen and phosphorus uptake and growth dynamics. LR development is influenced by hormone levels and external environment. In particular, auxin and abscisic acid coordinate with each other to maintain normal LR development. Of course, changes in the external environment are also important for root development, and they affect the intrinsic hormone levels of plants by affecting the accumulation and transport of hormones. For example, nitrogen, phosphorus, reactive oxygen species, nitric oxide, water, drought, light, and rhizosphere microorganisms affect LR development and plant tolerance in a variety of ways, including regulating hormone levels. This review summarizes the factors affecting LR development and the regulatory network and points out the direction for future research.

Microbiome-mediated signal transduction within the plant holobiont

Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant-microbe interactions and changes in plant physiology activated by signal transduction.

GIGANTEA regulates lateral root formation by modulating auxin signaling in Arabidopsis thaliana

Lateral root (LR) formation is a vital organogenetic process that determines the root architecture in plants. The number of root branches governs the degree of anchorage, efficiency of nutrients acquisition, and water uptake. The molecular pathways involved in LR formation have been extensively studied in Arabidopsis thaliana (At). A plant hormone, Auxin, is a key regulator of root development and promotes LR formation in plants. A plethora of Arabidopsis genes have been identified to regulate LR initiation, patterning, and emergence processes. Recently, the involvement of flowering time control pathways and circadian clock pathways in LR development has come to light, but the connecting link between these processes is still missing. We have established that GIGANTEA (GI), a key component of photoperiodic flowering, can regulate the formation of LRs in Arabidopsis. GI is known to be involved in red light signaling and circadian clock signaling pathways. Here, we report that over-expression of GI enhances LR formation in red light in At. Real-time PCR analysis shows that GI positively regulates the transcription of TRANSPORT INHIBITOR RESPONSE 1 (TIR1) which is an upstream component of auxin signaling. Furthermore, gi-100 mutant downregulates the LR initiation signaling gene, AUXIN RESPONSE FACTOR 7 (ARF7), and its downstream target gene, LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16). Hence, GI acts as a positive regulator of IAA14-ARF7-LBD16 modules during LR initiation. We have also checked the effect of GI on the expression of NAC1 and AIR3 genes which are controlled by TIR1 during LR formation. Our results show that GI induces the NAC1 transcription and its downstream gene, AIR3 expression, which leads to the enhancement of LR initiation. Taken together, our results suggest that GI controls the expression of TIR1 to govern auxin signaling during LR formation in presence of red light and GI can act as a link between circadian clock signaling, flowering time control pathways, light signaling, and lateral root development pathways.

Scion-to-Rootstock Mobile Transcription Factor CmHY5 Positively Modulates the Nitrate Uptake Capacity of Melon Scion Grafted on Squash Rootstock

It is generally recognized that the root uptake capacity of grafted plants strongly depends on the rootstocks' well-developed root system. However, we found that grafted plants showed different nitrate uptake capacities when different varieties of oriental melon scion were grafted onto the same squash rootstock, suggesting that the scion regulated the nitrate uptake capacity of the rootstock root. In this study, we estimated the nitrate uptake capacity of grafted plants with the different oriental melon varieties' seedlings grafted onto the same squash rootstocks. The results indicated a significant difference in the nitrate uptake rate and activity of two heterologous grafting plants. We also showed a significant difference in CmoNRT2.1 expression in the roots of two grafting combinations and verified the positive regulation of nitrate uptake by CmoNRT2.1 expression. In addition, the two varieties of oriental melon scion had highly significant differences in CmHY5 expression, which was transported to the rootstock and positively induced CmoHY5-1 and CmoHY5-2 expression in the rootstock roots. Meanwhile, CmHY5 could positively regulate CmoNRT2.1 expression in the rootstock roots. Furthermore, CmoHY5-1 and CmoHY5-2 also positively regulated CmoNRT2.1 expression, respectively, and CmoHY5-1 dominated the positive regulation of CmoNRT2.1, while CmHY5 could interact with CmoHY5-1 and CmoHY5-2, respectively, to jointly regulate CmoNRT2.1 expression. The oriental melon scion regulated the nitrate uptake capacity of the melon/squash grafting plant roots, and the higher expression of CmHY5 in the oriental melon scion leaves, the more substantial the nitrate uptake capacity of squash rootstock roots.

Signaling events for photomorphogenic root development

A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.

The central role of GmGLP20.4 in root architecture modifications of soybean under low-nitrogen stress

KEY MESSAGE

The GmGLP20.4 candidate gene plays an important role to improve soybean root architecture under low-nitrogen stress. The results lay the foundation for breeding low-nitrogen-tolerant soybean. Roots are fundamentally important for plant growth and development, facilitating water and nutrient uptake. Various abiotic and biotic factors significantly affect the root system architecture, especially low nitrogen (LN), but the molecular mechanism remains unclear. In this study, we identified GmGLP20.4, a germin-like protein (ubiquitous plant glycoproteins belonging to the Cupin superfamily) crucial for lateral root development and highly induced by LN stress in lateral roots of soybean. GmGLP20.4 overexpression increased root biomass through development of an improved root system in soybean under LN, whereas a significant decrease in root biomass was observed in the gmglp20.4 knockout mutant. Overexpression of GmGLP20.4 improved plant growth and root architecture in transgenic tobacco (Nicotiana tabacum) under LN. Natural variation of the GT-1 cis-element in the promoter (T to A) of GmGLP20.4 was strongly associated with its expression level under LN, and significantly increased LN-sensitive variation (type A) was observed in wild soybean compared to that in elite cultivars. Thus, type A variation in the promoter of GmGLP20.4 may have been a site of artificial selection during domestication. The GmGT1-16g gene was highly expressed under LN and showed an expression pattern opposite to that of GmGLP20.4. A luciferase complementation imaging assay revealed that the GmGLP20.4 promoter specifically binds to GmGT1-16g. In conclusion, GmGLP20.4 is involved in soybean root development and the natural variation of its promoter will be useful in modern intercropping systems or to improve nitrogen-use efficiency.