Suppression subtractive cDNA hybridization (SSH) was used to identify genes that are differentially up- and down-regulated in apples (Malus × domestica) in response to challenge with Erwinia amylovora (Ea). cDNA libraries were constructed from E. amylovora- and mock-challenged 'Gale Gala' apple leaf tissue at various time intervals after challenge treatment, ranging from 1 to 72 hours post inoculation (hpi) and utilized in SSH. A total of 432 non-redundant Malus ESTs isolated by SSH in response to E. amylovora challenge were characterized by bioinformatic analysis. Many ESTs identified following Ea-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 (24, 48, 72 hpi) in the infection process. For example, within the defense/stress functional category, ESTs representing several different PR proteins were first detected 48 hpi (up-regulated), whereas earlier defense/stress ESTs were primarily associated with oxidative and osmotic stress.
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