Rapid transcriptional response of apple to fire blight disease revealed by cDNA suppression subtractive hybridization analysis

Fire blight, caused by the bacterium Erwinia amylovora, is a destructive disease of many tree and shrub species of the Rosaceae. Suppression subtractive cDNA hybridization (SSH) was used to identify genes that are differentially up- and down-regulated in apple (Malus x domestica) in response to challenge with E. amylovora. cDNA libraries were constructed from E. amylovora- and mock-challenged apple leaf tissue at various time intervals after challenge treatment, ranging from 0.25 to 72 h post-inoculation (hpi), and utilized in SSH. Gel electrophoresis of PCR-amplified SSH cDNAs indicated a greater quantity and size diversity in the down-regulated EST population at early times after challenge (1 and 2 hpi) compared to early up-regulated sequences and to sequences down-regulated at later (24 and 48 hpi) times after challenge. A total of 468 non-redundant Malus ESTs isolated by SSH in response to E. amylovora challenge were characterized by bioinformatic analysis. Many of ESTs identified following E. amylovora challenge of apple were similar to genes previously reported to respond to bacterial challenge in Arabidopsis thaliana. The results indicate that there was a substantial early (1 and 2 hpi) transcriptional response in apple to fire blight disease involving both the down- and up-regulation of host genes. Additionally, genes identified responding to fire blight challenge early (1 and 2 hpi) differed from those identified later (25, 48, and 72 hpi) in the infection process.