Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Ruberti A. thaliana Intermediate molecular events in plant responses to canopy shade

ABSTRACT: Aim of the experiment is the analysis of early and late molecular events in plant response to canopy shade. To this end, gene expression changes were analysed in Arabidopsis seedlings after exposure to low R/FR light for 4 hours and 1 day. The experiment was designed to enable comparison between treated and untreated Arabidopsis seedlings.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Ida Ruberti

PROVIDER: E-MEXP-3266 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dynamics of the shade-avoidance response in Arabidopsis.

Ciolfi Andrea A Sessa Giovanna G Sassi Massimiliano M Possenti Marco M Salvucci Samanta S Carabelli Monica M Morelli Giorgio G Ruberti Ida I

Plant physiology 20130726 1

Shade-intolerant plants perceive the reduction in the ratio of red light (R) to far-red light (FR) as a warning of competition with neighboring vegetation and display a suite of developmental responses known as shade avoidance. In recent years, major progress has been made in understanding the molecular mechanisms underlying shade avoidance. Despite this, little is known about the dynamics of this response and the cascade of molecular events leading to plant adaptation to a low-R/FR environment. ...[more]

PMID: 23893169

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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

Ruberti A. thaliana Intermediate molecular events in plant responses to canopy shade

Publications

Dynamics of the shade-avoidance response in Arabidopsis.

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