Response to low R/FR light ratio in wt and brc1 mutant Arabidopsis axillary buds
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE27273 | GEO | 2013/02/28
SECONDARY ACCESSION(S): PRJNA137137
REPOSITORIES: GEO
Similar Datasets
Project description:To study the transcriptomic profile of wt and brc1 mutant axillary buds during the shade avoidance response, we simulated a canopy shade with a low R/FR light ratio. We treated plants with white light supplemented with far-red light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 146 μeinstein · m-2 seg-1) for 8 hours. Control plants were left for 8 hours in white light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 2.2 μeinstein · m-2 seg-1) . Six biological replicates of 7-8 plants were collected for each genotype and condition (wt WL, wt FR, brc1 WL, brc1 FR). Samples were compared wt WL vs wt FR and brc1 WL vs brc1 FR.
2013-02-28 | E-GEOD-27273 | biostudies-arrayexpress
Project description:Growth in dense stands induces shade avoidance responses. Late stages of stand development lead to low red:far-red (R:FR) and low blue light conditions. We studied gene expression in late stages of canopy development when both light signals were present, and studied gene expression in the single and combined light treatments.
2016-11-23 | GSE87770 | GEO
Project description:Plant architecture greatly depends on its branching patterns. Branches are formed from meristems initiated in the axils of leaves. Axillary meristems may develop immediately giving new shoots or they may become arrested after a short period of growth as dormant axillary buds. This decision is affected by endogenous and environmental factors. We are studying two Arabidopsis genes coding for TCP transcription factors, BRANCHED1 (BRC1) and BRANCHED2 (BRC2) that control this key decision. Several endogenous and environmental stimuli affect this process one of them is the quality of ambient light. Plants have developed sophisticated mechanisms that allow them to detect the presence of nearby plants and trigger responses of development to avoid the shade. This set of responses is known as shade avoidance. One response to this syndrome, with high agronomic relevance, is the suppression of branching. The genetic basis of this response is still largely unknown. Our goal is to carry out, in Arabidopsis, a systematic study of the genetic control of the removal of branching during the escape response of the shadow. We found that Arabidopsis plants produce fewer branches when grown at high density. We also found that the removal of high-density branch is accompanied by up-regulation of BRC1. On the other hand, short light treatment enriched in far-red (which simulate the shade plant) also cause an accumulation of BRC1 mRNA levels in plants grown at low density. Besides initial data off transcriptomic analysis (wt vs. brc1-2) indicate that BRC1 could be involved in signaling / response to light in the axillary buds. In this study we have identified several potential target genes of BRC1 involved in the response to light. One is PIL2 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 2), a gene that encodes a bHLH transcription factor that interacts with APRR1/TOC1. We are currently characterizing in more detail at the genetic and molecular level the BRC1 relationship with this and other potential target genes and their role in the control of branching patterns. The microarray analysis was performed using RNA samples obtained from three independent plant pools grown under identical conditions. The cDNA synthesized from RNA of wild type or brc1-2 plants grown either in white light (WT-WL, brc1-2-WL) or red+far red light (WT-FR, brc1-2-FR) was hybridized.
2014-05-11 | E-GEOD-23407 | biostudies-arrayexpress
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. Keywords: shade avoidance auxin brassinosteroid
2008-04-01 | GSE9816 | 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 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:Plant architecture greatly depends on its branching patterns. Branches are formed from meristems initiated in the axils of leaves. Axillary meristems may develop immediately giving new shoots or they may become arrested after a short period of growth as dormant axillary buds. This decision is affected by endogenous and environmental factors. We are studying two Arabidopsis genes coding for TCP transcription factors, BRANCHED1 (BRC1) and BRANCHED2 (BRC2) that control this key decision. Several endogenous and environmental stimuli affect this process one of them is the quality of ambient light. Plants have developed sophisticated mechanisms that allow them to detect the presence of nearby plants and trigger responses of development to avoid the shade. This set of responses is known as shade avoidance. One response to this syndrome, with high agronomic relevance, is the suppression of branching. The genetic basis of this response is still largely unknown. Our goal is to carry out, in Arabidopsis, a systematic study of the genetic control of the removal of branching during the escape response of the shadow. We found that Arabidopsis plants produce fewer branches when grown at high density. We also found that the removal of high-density branch is accompanied by up-regulation of BRC1. On the other hand, short light treatment enriched in far-red (which simulate the shade plant) also cause an accumulation of BRC1 mRNA levels in plants grown at low density. Besides initial data off transcriptomic analysis (wt vs. brc1-2) indicate that BRC1 could be involved in signaling / response to light in the axillary buds. In this study we have identified several potential target genes of BRC1 involved in the response to light. One is PIL2 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 2), a gene that encodes a bHLH transcription factor that interacts with APRR1/TOC1. We are currently characterizing in more detail at the genetic and molecular level the BRC1 relationship with this and other potential target genes and their role in the control of branching patterns.
2014-05-11 | GSE23407 | GEO
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.
2012-05-01 | GSE35700 | 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:Arabidopsis is a shade avioding plant. Under simulated shade light with reduced red-to-far red (R:FR) ratio around 0.7, hypocotyls of Arabidopsis seedlings elongate, which is one of the typical shade avoidance responses.We discovered that when the R:FR ratio further decreases to around 0.1 (strong shade), the shade-induced elongation of hypocotyl is abolished and phytochrome A (phyA) mediates this response.In this study, we aim to examine the difference between shade and strong shade treatment and uncover the role of phyA in regulating the shade avoidance responses.
2019-12-21 | GSE55899 | GEO