Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA347371 | ENA |
REPOSITORIES: ENA
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Project description:The goal of this work was to investigate oxidative stress responses of Arabidopsis to low red to far-red ratios of light as a signal of competition using a biological weedy and an artificial source of far-red light. More specifically, elucidation of the signaling role of singlet oxygen in Arabidopsis under low red-to far-red light environments was the major objective of this work. Oxidative stress responses of Arabidopsis to low red (R) to far-red (FR) signals (R:FR ≈ 0.3), generated by a biological weedy and an artificial source of FR light, were compared with a weed-free control (R:FR ≈1.4). In the low R:FR treatments, induction of the shade avoidance responses coincided with increased singlet oxygen (1O2) production and decreased level of superoxide and superoxide dismutase activity. Although the increase of 1O2 was not due to protochlorophyllide accumulation and did not result in cell death, treatments with the 1O2 generator 5-aminolevulinic acid increased sensitivity to cell death. Transcriptome responses minimally resembled those reported in four Arabidopsis 1O2 generating systems such that only few genes (6 out of 1931) were consistently up-regulated supporting the specificity of 1O2 signaling. Moreover, suppressors of jasmonate accumulation, including the 1O2-responsive amidohydrolase ILL6, the sulfotransferase ST2a, which are involved in prioritization of elongation growth versus defense were consistently up-regulated. Our data support a model in which photoreceptors connect low R:FR light cues to the JA signaling pathway. Repression of bioactive JAs via the amidohydrolase ILL6, and sulfotransferase ST2a may promote the shade avoidance (versus defense) and 1O2 acclimation (versus cell death) responses to competition cues.
2022-09-14 | GSE213185 | GEO
Project description:Background: Potato (Solanum tuberosum L.) is the fourth largest food crop worldwide with significant economic value and importance for food security. Shade avoidance syndrome (SAS) considerably affects crop architecture and productivity in high-density planting systems; however, its molecular mechanisms in potato remain poorly understood. Methods: Potato seedlings were subjected to four light treatments simulating different shade signals: white light (control, WL), low blue light (LBL, simulating blue light attenuation by plant canopies), low red:far-red ratio (WL+FR, simulating far-red reflection from neighboring plants), and their combination (LBL+FR, simulating complete plant shade environment). We conducted a comprehensive study integrating morphological characterization, leaf anatomical analysis, hormone quantification, transcriptome sequencing, and metabolite profiling. Results: Morphological analysis revealed that WL+FR primarily induced internode elongation (+20.0%) and leaf hyponasty, while LBL promoted stem elongation through increased node production (+36.3%). When combined, these signals (LBL+FR) synergistically enhanced stem elongation by 79.3%. Anatomical examination showed that LBL-treated leaves formed thickened palisade tissue layers (176.34 μm) with 6-7 layers of spongy tissue, whereas WL+FR resulted in thinner leaves (151.22 μm). Transcriptomic analysis identified 6,057 differentially expressed genes enriched in photosynthesis, hormone signaling, and carbohydrate metabolism pathways. A total of 1,168 differentially accumulated metabolites were detected across treatments, particularly organic acids and lipids associated with TCA (tricarboxylic acid) cycle and starch-sucrose metabolism. Weighted gene co-expression network analysis (WGCNA) identified PHYTOCHROME A (PHYA) as the central hub gene coordinating SAS responses under combined light stress, significantly diverging from the PHYB-centric model established in Arabidopsis.
2025-12-16 | GSE313166 | GEO
Project description:Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, there is reduced branching, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance outputs. Here we describe SAV3, an aminotransferase, and show that SAV3 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway can be rapidly deployed to biosynthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance. Experiment Overall Design: Wild type Col-0, sav3-2 and sav1-1 seedlings were used here. They were treated with or without 1hr of low R:FR light (R:FR ratio=0.7). Three independent biological replicates were used.
2008-06-16 | E-GEOD-9816 | biostudies-arrayexpress
Project description:In dense stands,the earliest neighbor response is induced by touching,leading to shade avoidance. During light competion the R:FR distribution is not homogenous, leading to local differences in light quality (R:FR) within the same leaf. Hyponasty is induced by FR-signaling in the lamina tip, which then induces local cell growth in the petiole base. Likewise, local touching of the leaf tip induces a similar phenoype. We studied gene expression in Arabidopsis, exposed to supplemental-FR in the lamina tip and in whole rosette plant. We harvested the lamina tip and the petiole base after 5h of the treatments (white-light, supplemeted-FR in the lamina tip (local FR) and rossete plants exposed to low R:FR (whole plant FR))
2017-06-26 | GSE98643 | GEO
Project description:In plants, an increase in resource allocation to growth (primary metabolism) associated with the presence of neighbors is likely to reduce defense-related production (secondary metabolism), making plants more vulnerable to herbivory. Even though there is increasing evidence supporting this “trade-off hypothesis”, the underlying mechanisms are still unclear. Far red (FR) radiation reflected from plant tissues serves as an early warning signal of future competition, triggering a suite of plastic morphological adjustments that improve plant’s ability to compete for light in crowded populations. Recent evidence from our lab showed that, when competition signals are present, plant defenses are severely reduced. Besides direct effects of herbivory and competition signals on target plants, second order effects occurs on neighboring plants through plant volatiles (PVs) communication. PVs play a key role in plant-plant and plant-insect interactions, changing its content and composition in response to environmental conditions. To increase our understanding of the molecular mechanisms underlying those interacting signaling webs, we performed a field study with tomato plants (cv Moneymaker), in which plants of EMITTER plots (six plants plot-1) were subjected to herbivory (nine larvae of Spodoptera eridania plant-1) and competition signals (increased FR radiation) in a factorial design. Light treatment started 28 days after sowing (DAS), and herbivory treatment and volatiles conduction started 34 DAS. Volatiles were conducted from EMITTER to RECEIVER plots (five plants plot-1) using a 5 inch, 1.4 m long tube fitted with a computer-type fan. 40 and 45 DAS, larval performance was measured on EMITTER plots as well as naturally-occurring insect colonization on RECEIVER plots. Finally (46 DAS), samples for bulk phenolic content were taken on every plot, and plant material from 4th and 5th leaves was collected for microarray analysis. There were three real biological replicates. Keywords: Reference design
2008-02-13 | GSE10486 | GEO
Project description:Low R:FR signaling through phytochromes induces shade avoidance responses, including petiole elongation. Salicylic acid-mediated defense against pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and SA at the global gene expression level in Arabidopsis thaliana. Plants were exposed for 2 h. to the following treatments: high R/FR with mock spray, low R/FR with mock spray, high R/FR with SA spray, low R/FR with SA spray. Gene expression was determined in petioles.
2013-04-03 | E-GEOD-45728 | biostudies-arrayexpress
Project description:Low reduced red:far-red ratio [R:FR] signaling through phytochromes induces shade avoidance responses, including petiole elongation. Jasmonic acid-mediated defense against herbivores and pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and JA at the global gene expression level in Arabidopsis thaliana. Plants were exposed for 2 h. to the following treatments: high R/FR with mock spray, low R/FR with mock spray, high R/FR with JA spray, low R/FR with JA spray. Gene expression was determined in petioles.
2012-04-30 | E-GEOD-35700 | biostudies-arrayexpress
Project description:Hypocotyl and cotyledon transcriptome in Arabidopsis thaliana treated with 1 ppm ethylene and shade (low PAR, low blue and low R:FR)
| PRJNA325269 | ENA
Project description:Cryptochromes interact directly with PIFs to control plant growth in limiting blue light
| PRJNA255977 | ENA