Spotlight and whole-plant far-red enrichment at sub-organ-specific level
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE98643 | GEO | 2017/06/26
SECONDARY ACCESSION(S): PRJNA385808
REPOSITORIES: GEO
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Project description:Arabidopsis plants transfer information from the leaf tip to the petiole base to induce adaptive upward leaf movement upon neighbour detection through Far-Red light enrichment in the leaf tip. To determine how a distally derived signal can specifically regulate growth in the abaxial petiole we analysed the transcriptome in the leaf tip and abaxial-adaxially split petiole sections during the first hours of far-red enrichment.
2022-12-20 | GSE218944 | GEO
Project description:In dense plant stands, the ratio between red and far-red (R:FR) light declines and shade intolerant species will respond to this cue for future shade by inducing the shade avoidance syndrome (SAS), enabling them to outgrow their neighbours. Shade tolerant species from the forest understory are unable to outgrow neighbouring trees and will suppress SAS. Although the molecular mechanisms underlying SAS are well studied in various species, mechanisms of SAS-suppression in shade tolerant species have rarely been studied. We applied RNA sequencing on Geranium pyrenaicum and G. robertianum, two wild species with contrasting growth responses to low R:FR light. G. pyrenaicum strongly induces petiole elongation when exposed to low R:FR light, at any time of the photoperiod. Contrastingly, G. robertianum only induces this response early in the day, and suppresses petiole growth in low R:FR light at the end of the photoperiod, which results after 24 hours in a net difference with control treatments of zero. We compared expression patterns in the most apical (most responsive) part of the second petioles, in two-week-old Geranium plants (two leaf stage) after 2 and 11.5 hours of far-red light enrichment. This way, we identified a number of novel candidate regulators of shade avoidance, and differential phytochrome control of plant immunity genes in the two species. For de-novo assembly of the reference transcriptomes, we pooled petiole- and leaf lamina tissue exposed to normal white light (180 mol m-2 s-1 PAR, R:FR 1.8, ± 60 mol m-2 s-1 blue light), low R:FR light (0.2), blue-depleted light (± 4 mol m-2 s-1 blue) and green shade (50 mol m-2 s-1 PAR, R:FR 0.45, ± 13 mol m-2 s-1 blue) for 2, 11.5 and 24 hours. Libraries of these samples were normalized, Illumina sequenced, and together with sequences of non-normalized petiole samples of the expression analysis constructed into a reference transcriptome for each species, using the Trinity protocol. Transcripts were clustered into orthologue clusters using the ortho-MCL clustering technique. Non-normalized libraries of samples (control vs. low R:FR light, 2 and 11.5 hours after start of the treatment) were sequenced and aligned to the newly assembled transcriptomes. Read counts were summed per orthologue cluster before statistical analysis was proceeded.
2017-02-01 | E-MTAB-5371 | biostudies-arrayexpress
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:High humidity greatly influences plant growth and development by triggering adaptive physiological responses such as leaf hyponasty. Recent studies identified CNGC2/4-mediated Ca2+ influx and CAMTA2/3-mediated transcription as essential for this process, but the upstream regulators that control these pathways remain unknown. Here, we show that the receptor-like kinase FERONIA (FER) is required for Arabidopsis adaptation to high humidity. Transcriptomic profiling revealed rapid induction of CNGC2, CAMTA targets, and pectin remodeling genes in wild-type plants but not in fer-4 loss of function mutants. A targeted mutant screen confirmed that FER and its co-receptor LORELEI-LIKE GPI-ANCHORED PROTEIN1 (LLG1) are essential for humidity-induced hyponasty. Whole-plant Ca²⁺ imaging demonstrated that high humidity triggers conserved cytosolic Ca²⁺ elevations across species, including petiole-localized Ca²⁺ waves in Arabidopsis that precede hyponastic movement by ~2 h. These signals were significantly attenuated in fer-4, providing a mechanistic explanation for its transcriptional and physiological defects. Together, our findings identify FERONIA as a key upstream component of a sensing mechanism linking extracellular high humidity to Ca²⁺ signaling, cell wall remodeling, and adaptive leaf movement.
2025-09-30 | GSE308941 | GEO
Project description:Plants grown under a canopy recognize changes in light quality and modify their growth patterns; this modification is known as shade avoidance syndrome. In leaves, leaf blade expansion is suppressed, whereas petiole elongation is promoted under the shade. However, the mechanisms that control these responses are largely unclear. Here, we demonstrated that both auxin and brassinosteroid (BR) are required for the normal leaf responses to shade. The microarray analysis of leaf blades and petioles treated with end-of-day far-red light (EODFR) revealed that almost half of the genes induced by the treatment in both parts were previously identified as auxin-responsive genes. Likewise, BR-responsive genes were overrepresented in the EODFR-induced genes. Hence, the auxin and BR responses were elevated by EODFR treatment in both leaf blades and petioles, although opposing growth responses were observed in these two parts. The analysis of the auxin-deficient doc1/big mutant and BR-deficient rot3/cyp90c1 mutant further indicates that auxin and BR were equally required for the normal petiole elongation response to the shade stimulus. In addition, the spotlight irradiation experiment revealed that phytochrome in leaf blades but not that in petioles regulated petiole elongation, which was probably mediated through regulation of the auxin/BR responses in petioles. On the basis of these findings, we conclude that auxin and BR cooperatively promote petiole elongation in response to the shade stimulus under the control of phytochrome in the leaf blade. The WT seedlings were grown for 19 days under continuous white light condition before experimental treatment with three light conditions. Seedlings were either maintained in white light for 2 h (WL), incubated in the dark condition for 2 h (D), or experienced a pulse irradiation of FR light before incubated in the dark condition for 2 h (FRD). Total RNAs were separately prepared from leaf blades and petioles after each light treatment. Three independent biological replicates were used.
2009-10-31 | E-GEOD-17845 | biostudies-arrayexpress
Project description:Local light signalling at the leaf tip drives remote differential petiole growth through auxin-gibberellin dynamics
| PRJNA906171 | ENA
Project description:Background: The growth and development of leaf and petiole have an important influence on the photosynthesis of plants. The research on molecular mechanism of leaf and petiole development is of great significance, whether it is to improve plant photosynthetic efficiency, cultivate varieties with high photosynthetic efficiency, or improve the yield of crops using leaves as food organs. In this study, we aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). These data were then used to construct competitive endogenous RNA (ceRNA) networks, which can provide valuable information for better understanding the mechanism of leaf and petiole development. Results: In this study, the leaf and petiole of the baby Chinese cabbage inbred line ‘PHL’ were used as research materials for whole-transcriptome sequencing. A total of 10646 differentially expressed (DE) mRNAs, 303 DE lncRNAs, 7 DE circRNAs, and 195 DE miRNAs were identified between the leaf and petiole. Some transcription factors or proteins that play important roles in leaf and petiole development were identified, such as xyloglucan endotransglucosylase/hydrolase (XTH) protein, expansion protein, TCP15 transcription factor, bHLH transcription factor, LOB domain protein, cellulose synthase (CESA), MOR1-like protein, and plant hormone biosynthesis related genes. Additionally, we constructed a leaf and petiole development-related ceRNA regulatory network, and obtained 85 pairs of ceRNA relationships, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA and 2 DEmiRNA-DEcircRNA. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaf and petiole of baby Chinese cabbage were screened from transcriptome data for subcellular localization analysis and overexpression transgenic verification. The results showed that BrLSH1, BrLSH2 and BrLSH3 were nucleoprotein and BrLSH2 has an obvious inhibitory effect on the growth and development of Arabidopsis thaliana. Conclusions: Our results revealed the potential mRNAs and non-coding RNAs (ncRNAs) involved in leaf and petiole development, which laid a foundation for further research on the molecular mechanism of leaf and petiole development in Chinese cabbage.
2022-12-29 | GSE218959 | GEO
Project description:Shade avoidance syndrome (SAS) is a strategy of major adaptive significance that includes the elongation of vegetative structures and leaf hyponasty. Major transcriptional rearrangements underlie for the reallocation of resources to elongate vegetative structures and redefine the plant architecture under shade to compete for photosynthesis light. BBX28 is a transcription factor involved in seedling de-etiolation and flowering in Arabidopsis thaliana, but its function in the SAS is completely unknown. Here we studied the function of BBX28 in the regulation of gene expression under simulated shade conditions.
2024-03-15 | GSE217723 | GEO
Project description:Growth in dense stands induces shade avoidance responses. Early responses to neighbors seem to be assoctaed with touch, not light signalling. We studied gene expression in petioles during early canopy development when leaf hyponasty was visible but altered phytochrome signalling was not yet detectable.
2012-09-04 | GSE39010 | GEO
Project description:SA0420 is a stable rice (Oryza sativa L.) mutant exhibits multiple traits including a leaf-tip yellowing (YLT), a taro fragrance (or aroma, A), a reduced panicle number (PN), spikelet number (SN), plant height (PH), days to heading (DH), filled grain weight (FGW), and fertility rate (FR), different from those of a local cultivar TNG67. Correlation analysis on F2 progenies of SA0420 and TNG67 revealed that except for aroma which is inheritated independently, phenotypes including YLT, PN, SN, PH, and FGW are tightly associated with each others, indicating a control simultaneously by pleotropic gene. Among those phenotypes, YLT appears the earliest at vegetative stage, therefore may act as a predisposing factor that give rise to other phenotypes. Genetic analysis suggested that YLT is controlled by a single recessive gene. By analyzing the recombinant inbreed lines (RILs) that produce YLT and normal green (G) progenies in a 1:3 ratio, the phenotypes associated with YLT were further confirmed. To investigate the molecular events of leaf-tip yellowing, microarray analyses were performed to compare the gene expression profiles between YLT and G plants of RILs. Clustering of genes according to their involved metabolic pathways revealed that various photosynthesis and carbon fixation gene expressions are lower (~55~75%) in YLT than in G plants, consistent with the observation that photosynthesis rate of SA0420 was only 60% to that of TNG67. Moreover, higher expressions of oxidative phosphorylation-related genes indicated that not only the reduced synthesis rate but also the elevated energy consumptions may synergistically decrease the growth vigor of SA0420. Dissection of the mature leaf revealed that chlorophyll is drastically reduced in the leaf-tip of SA0420 while carotenoids remain stable. This explains the appearance of leaf-tip yellowing and recall an analogy of early senescence. Indeed, many senescence-associated genes (SAG) were found to be up-regulated in SA0420. Experiment Overall Design: To investigate the molecular events of leaf-tip yellowing, microarray analyses were performed to compare the gene expression profiles between YLT and G plants of RILs.
2008-11-06 | E-GEOD-10872 | biostudies-arrayexpress