ARS | Publication request: Computational Identification of Candidate Genes Involved in Response to Fire Blight in Apples

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: December 1, 2006
Publication Date: N/A

Technical Abstract: Fire blight (Erwinia amylovora) is a destructive bacterial disease affecting plants in the Rosaceae including apple, pear, and quince. The disease is common in North America, and kills blossoms, shoots, limbs, and, sometimes, entire trees. Bioinformatics tools were used in collaboration with a NRI-funded project focused on functional genomics to characterize apple response to fire blight. Publicly available apple ESTs uniquely associated with E. amylovora-infected apple and cDNA suppression subtractive EST libraries specific to resistant and susceptible apple cultivars at various times after innoculation were analyzed. Vector-screening tools were custom-modified to identify EST contamination. Computational methods (EST clustering) were developed for identifying genes expressed uniquely in disease-challenged tissue. Comparisons with genes associated with Arabidopsis response to Pseudomonas syringae infection were done, and identification of additional candidate genes via annotation. These predictions are being tested via the NRI project using RNA silencing. The expression of the genes identified will also be ascertained through collaboration with existing microarray projects.