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- 290-MICROARRAY GENE EXPRESSION ANALYSIS OF GRAPE PLANTS IN RESPONSE TO XYLELLA FASTIDIOSA INFECTION Project

Transcriptional profiling using a custom high-density microarray chip of 20,020 Vitis transcripts showed significant variations in responses between the susceptible and resistant genotypes to Xylella fastidiosa (Xf) infection. Differentially expressed transcripts reflecting spatial and temporal responses to Pierce’s disease (PD) involved in metabolic processes such as diseases resistance, water stress, photosynthesis and cell wall synthesis were identified. The results suggest that Vitis responses to Xf are genotype and tissue dependent, and are stage specific. VitisExpDB is an online MySQL-php driven relational database that houses annotated EST data. The database will provide genomic resource to grape community for functional analysis for both vinifera and non-vinifera grape varieties and aid in the grape genome annotation. INTRODUCTION The impact of Pierce’s disease (PD) on the California grape industry has been significant since the introduction and establishment of a more effective vector, Homalodisca vitripennis, the glassy-winged sharpshooter (GWSS) (Almeida and Purcell 2003). Development of resistance in grape is stymied by the relatively limited amount of genetic and molecular information regarding genotype specific resistance to PD infection (Davis et al. 1978). From genotypic screening and genetic mapping studies, it was concluded that a dominant allele controls PD resistance and recently, Krivanek et al. (2006) identified a major quantitative trait locus that controls PD resistance and denoted it as ‘Pierce’s disease resistance 1’ (PdR1). The above studies confirm that the genetic basis of PD resistance in grapes varies from tolerance to resistance and suggest that host responses to the pathogen are genotype dependent. Further, in the PD resistant genotypes, differential responses between stem and leaf tissues were also noted (Krivanek and Walker, 2005). The results from these studies prompted study of molecular basis of this host / pathogen interaction. Plants respond to pathogen attack through a variety of signaling pathways consisting of a large number of regulatory as well as effector genes. Microarrays facilitate automated analysis of transcriptional profiling data to enable complete understanding of such gene function and interactions. The goal of this study was to identify and characterize the molecular events in the grape / Xylella fastidiosa (Xf) interaction using genome wide transcriptome profiling between resistant and susceptible genotypes and among the different tissue types. OBJECTIVES 1. Microarray gene expression analysis. 2. Develop of a grape transcriptional relational database. RESULTS Objective 1 Microarray gene expression analysis. Custom microarray chip design: Previously, we have characterized transcriptomes (5,794 ESTs) from 12 tissue specific (stem, leaf and shoot) subtractive suppression hybridization (SSH) libraries. All the sequenced ESTs that are at least 100 bp in length (5421 ESTs) were submitted to the NCBI’s ESTdb under the accession numbers DN942225 to DN947645. These ESTs and all the other EST sequences publicly available till July of 2005 were analyzed to deduce a non-redundant set of 20,020 ESTs with 1,947 from the SSH libraries, including 40 from the cDNA-AFLP experiments, 10,014 from V. vinifera, 5,470 from V. shuttleworthii, 1,219 from V. aestivalis, 780 from V. rupestris x V. sp and 588 from V. riparia. Nine individual 60-mer probes were designed for each EST. A total of 191,450 probes were selected for the entire set and there were two spots for each probe on the slide totaling 382,900 spots per slide.