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AOBPreview originally published online on July 20, 2005
Annals of Botany 2005 96(4):661-668; doi:10.1093/aob/mci218
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© The Author 2005. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org

The Use of Microarrays to Study the Anaerobic Response in Arabidopsis

SILVIA GONZALI1, ELENA LORETI2, GIACOMO NOVI1, ALESSANDRA POGGI1, AMEDEO ALPI1 and PIERDOMENICO PERATA3,*

1 Department of Crop Plant Biology, University of Pisa, Via Mariscoglio 34, 56124 Pisa, Italy, 2 Institute of Biology and Agricultural Biotechnology, CNR, Via del Borghetto 80, 56100 Pisa, Italy and 3 Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà, 33, 56127 Pisa, Italy

* For correspondence. E-mail p.perata{at}sssup.it

Received: 19 October 2004    Returned for revision: 19 December 2004    Accepted: 17 January 2005    Published electronically: 20 July 2005

• Background and Aims The use of microarrays to characterize the transcript profile of Arabidopsis under various experimental conditions is rapidly expanding. This technique provides a huge amount of expression data, requiring bioinformatics tools to allow the proposal of working hypotheses. The aim of this study was to test the usefulness of this approach to examine the anaerobic response of Arabidopsis by evaluating the reliability of microarray data sets and by interrogation of microarray databases for the expression data of a set of anoxia-inducible genes.

•Methods User-driven software tools that display large gene expression datasets onto diagrams of metabolic pathways were used. The Genevestigator software was used to explore the expression of anoxia-inducible genes throughout the life cycle of Arabidopsis as well as relative to plant organs. T-DNA tagged mutants for selected genes identified from our microarray analysis were searched in the Arabidopsis thaliana Insertion Database, looking for insertional mutants from the Salk collection.

•Key Results The results indicate that microarray data can provide the basis for new hypotheses in the field of plant responses to anaerobiosis and also provide knowledge for a targeted screening of Arabidopsis mutants.

•Conclusions Research on plant responses to anaerobiosis can enormously benefit from the microarray technology.

Key words: Anaerobiosis, anoxia, Arabidopsis thaliana, microarray, mutants


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