Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression data from low R:FR - JA crosstalk in Arabidopsis

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Ronald Pierik

PROVIDER: E-GEOD-35700 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Low red/far-red ratios reduce Arabidopsis resistance to Botrytis cinerea and jasmonate responses via a COI1-JAZ10-dependent, salicylic acid-independent mechanism.

Cerrudo Ignacio I Keller Mercedes M MM Cargnel Miriam D MD Demkura Patricia V PV de Wit Mieke M Patitucci Micaela S MS Pierik Ronald R Pieterse Corné M J CM Ballaré Carlos L CL

Plant physiology 20120227 4

Light is an important modulator of plant immune responses. Here, we show that inactivation of the photoreceptor phytochrome B (phyB) by a low red/far-red ratio (R:FR), which is a signal of competition in plant canopies, down-regulates the expression of defense markers induced by the necrotrophic fungus Botrytis cinerea, including the genes that encode the transcription factor ETHYLENE RESPONSE FACTOR1 (ERF1) and the plant defensin PLANT DEFENSIN1.2 (PDF1.2). This effect of low R:FR correlated wi ...[more]

PMID: 22371506

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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, Â± 60 mol m-2 s-1 blue light), low R:FR light (0.2), blue-depleted light (Â± 4 mol m-2 s-1 blue) and green shade (50 mol m-2 s-1 PAR, R:FR 0.45, Â± 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.

Dataset Information

Expression data from low R:FR - JA crosstalk in Arabidopsis

Publications

Low red/far-red ratios reduce Arabidopsis resistance to Botrytis cinerea and jasmonate responses via a COI1-JAZ10-dependent, salicylic acid-independent mechanism.

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