2006 Annual Report 4d.Progress report. This report serves to document research conducted under a specific cooperative agreement between ARS and University of California, Davis. Additional details of research can be found in the report for the parent project 5302-22000-007-00D Epidemiology and Management of Xylella fastidiosa (Xf)-caused Diseases and Xf Insect Vectors. A custom microarray gene chip based on our expressed sequence Tags (ESTs) and the publicly available EST sequences was designed. The chip consisted of all currently available ESTs from Vitis varieties and species with total 191,450 probes per chip. A two-color labeling method (Cy5 and Cy3) was used for 36 gene chip experiments representing two grape genotypes (resistant and susceptible genotypes), two treatments (healthy and infected), two tissue types (leaf and stem), three biological replicates and three stages of the disease development (early, mid and late). Data representing raw spot intensities generated by the GenePix software were analyzed using the SAM microarray analysis software to generate fold differences and q-values. Clustering of the significantly differentially expressed genes was carried out using TMEV software. Broad spectrum and presumably some non-specific plant responses were observed for defense and water stress related expression in the susceptible genotype. Current data analyses clearly demonstrated that majority of responses did not overlap susceptible genotype with the resistance genotype.