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BITS2007 Meeting
BITS2007 Meeting



26-28 April 2007 Napoli, Italy

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A global expression analysis of the shade avoidance response in Arabidopsis thaliana
 
Motivation
Crop productivity depends on the acquisition of resources and their distribution
within the plant to harvestable components. Resource allocation is highly plastic,
and can be regulated by many environmental factors. Temperature and water
availability can exert a profound influence on plant shape, affecting overall size as
well as the number and size of different organs. However, the major determinant of
plant architecture in the field is the response of the plant to signals from the
light environment. Plants growing in close proximity exhibit the shade avoidance
syndrome in response to reflected far-red (FR) radiation from neighbours. Shade
avoidance results in elongated internodes, reduced branching, weaker leaf
development, accelerated flowering and diminished fruit set. Shade avoidance is a
strategy of major adaptive significance to plants in natural communities,
particularly to the angiosperms from which most of the crop species have been
developed. However, the re-allocation of resources to competitive growth reduces
their availability for storage and reproduction, leading to diminished crop
productivity. To develop effective strategies that increase crop yields under high
density growth conditions, a molecular description of the shade avoidance response is
an important initial step. To this end, a global approach was used to highlight
expression changes induced by FR-rich light in Arabidopsis, taking advantage of all
the bioinformatics tools developed for this model organism.


Methods
Early and late events of the shade avoidance response in Arabidopsis were
investigated by means of Affymetrix Arabidopsis Genome GeneChip array (ATH1) analyses
on young seedlings exposed to low red (R)/FR light for short (1, 4 hours) and
prolonged (1, 4 days) times. After identification of statistically significant low
R/FR-responsive genes (one-way ANOVA, Student`s t-test with FDR= 0.05),
Genevestigator meta-profile analyses was used to study expression patterns across
different ontology categories. Functional classification of low R/FR regulated genes
was carried out by means of The Arabidopsis Information Resource (TAIR), a
comprehensive database of genetic, molecular and bioinformatics data for this plant.
Moreover, we analysed groups of co-expressed genes to identify shared regulatory
motifs. To this aim, we implemented Perl scripts to analyse putative promoter regions
of low R/FR-regulated genes and identify over-represented promoter elements
(http://pegaso1.bio.uniroma1.it/msblab/PLACE.php). Known plant promoter elements and
their annotation were downloaded from the PLACE database. For each set of n
co-expressed genes, we compared the number of occurrences for each motif in PLACE
against the average number of occurrences within 1,000 randomly generated sets of n
promoters. The one-tailed p-value for each motif is based on the Z-score of the
difference of the actual word count of the promoter set (Ctrue) minus the mean count
from the 1,000 surrogates (Crand) relative to the SD from the 1,000 surrogates
(SDrand) [i.e., Z=(Ctrue - Crand)/SDrand].


Results
The transcriptome analysis of Arabidopsis seedlings briefly exposed to low R/FR
revealed a rapid induction of a large number of genes functionally involved in light
and hormone signalling. Strikingly, auxin, gibberellin and brassinosteroid pathways
are up-regulated whereas cytokinin signalling is down-regulated. These changes in
hormone pathways are consistent with the enhanced elongation growth of stem-like
organs as well as with the reduced proliferative activity of leaf-like organs.
Remarkably, promoter analyses showed an evident over-representation for light and
hormone signalling related regulatory motifs, giving a further confirmation on the
prominent role of these pathways in shade avoidance responses. Interestingly,
transcriptome analysis of seedlings exposed to prolonged low R/FR revealed that gene
expression changes in hormone and light pathways are transient, implying that
persistency of the signal results in plant acclimation. Taken together, our data
underline the marked difference between the early and delayed events of the shade
avoidance response. The first ones are characterised by a strong induction of genes
encoding regulatory molecules which eventually trigger the developmental changes
caused by low R/FR exposure, whereas the second ones are characterised by broader and
more complex changes in gene expression aimed to sustain the growth of the plant even
in adverse light conditions.
 
Id: 139
Place: Napoli, Italy
Centro Congressi "Federico II"
Via Partenope 36
Napoli
Starting date:
-- not yet scheduled --   
Duration: 01h00'
Contribution type: Poster
Primary Authors: CIOLFI, Andrea (Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy; National Research Institute for Food and Nutrition, 00178 Rome, Italy)
Co-Authors: SASSI, Massimiliano (Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy)
SESSA, Giovanna (Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy)
SALVUCCI, Samanta (Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy)
UVA, Paolo (Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy; present address: Istituto di Ricerche di Biologia Molecolare, Merck Research Laboratories, 00040 Pomezia, Rome, Italy)
BECKER, Jorg (Affymetrix Core Facility, Instituto Gulbenkian de Ciencia, 2780-156 Oeiras, Portugal)
MORELLI, Giorgio (National Research Institute for Food and Nutrition, 00178 Rome, Italy)
RUBERTI, Ida (Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy)
Presenters: CIOLFI, Andrea
 
Included in session: Poster Session
Included in track: Gene expression and system biology
 




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