Gene expression profiling in tomato plants infected by four combinations of Cucumber mosaic virus and its satellite RNAs: A microarray analysis

An analysis of transcriptional changes in tomato plants, induced by the infection of Cucumber mosaic virus, alone or in combination with satellite RNA (satRNA) variants, has been made by microarray analysis. The analysis was performed on the newly developed CombiMatrix platform at the University of Verona, on a tomato chip carrying 20200 specific probes in quadruplicates from assembly of Tentative Consensus of the last Tomato Gene Index (LeGI), release 11.0 (June 21, 2006). The CombiMatrix CustomArray technology is characterized by an exclusive in situ oligo (up to 40 mers) synthesis driven by electrochemistry and by the reusability of the same microarray chip, all factors that confer high flexibility to the system and reduce remarkably the costs of microarray analysis. Tomato plants cv. UC82 were infected with the aggressive strain CMV-Fny and three more strains, in which CMV-Fny was associated with three different satRNAs (benign variant: CMV-Fny/Tfn-satRNA; stunting variant: CMV-Fny/TTS-satRNA; necrogenic variant: CMV-Fny/77-satRNA). Mock-inoculated plants were used as negative controls. Gene expression was examined at 2 and 9 days post inoculation, to analyse transcriptional changes associated with the different disease phenotypes in both locally and systemically infected leaf tissues. Hybridisations were carried out with samples deriving from three independent biological replicates. Differentially expressed genes were selected and analysed using the multi experiment Significance Analysis of Microarray test, and gene clustering was performed using Genesis software. This is the first time that the CombiMatrix platform for microarray analysis has been applied to the study of tomato-virus interactions.