Arabidopsis 2010: Expression Profiling of Plant Disease Resistance Pathways

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Plants respond to pathogen attack through a variety of signaling pathways consisting of a large number of regulatory as well as effector genes. During the past several years, many defense-related genes have been identified through genetic analysis conducted in Arabidopsis thaliana. Importantly, Arabidopsis exhibits all of the major kinds of defense responses present in other plants. Although a relatively large number of Arabidopsis defense-related genes have been identified, progress in developing overall explanatory models of plant-pathogen interactions is currently limited by two major experimental roadblocks. First, most of the phenotypic tests that have been used to characterize pathogen-host interactions do not have sufficient discriminatory power to assign defense-related genes to specific signal response pathways. To circumvent this limitation, large-scale transcript profiling analyses will be carried out on appropriately selected Arabidopsis defense-related mutants, including double and triple mutants. Combining genetic epistasis analysis with genomic technologies should lead to the development of a much more detailed model of how the various defense-related genes function and interact in combating pathogen attack. The second factor limiting the understanding of the plant defense response is that it is simply not possible to analyze the overwhelming volume of current data using conventional methods. The large volume of microarray data that will be generated in the near future compounds this problem. Moreover, data from different laboratories are not directly comparable because standardized experimental conditions are not employed. To help mitigate the problems associated with the analysis of large data sets, a sophisticated web-accessible plant-microbe interaction database (PMIDB) will be created to provide a common repository and standardized format for experimental data. The specific aims of the project are to:1) Use transcript-profiling analysis to identify Arabidopsis defense-related genes and construct a custom microarray (pathoarray) enriched for defense-related genes (A list the genes identified so far can be found at http://genetics.mgh.harvard.edu/ausubelweb/nsf2010/NSF_2010.html). These custom pathoarrays will be made available to the Arabidopsis community at a nominal cost with the expectation that the experimental results generated using these pathoarrays will be deposited in PMIDB.2) Use the pathoarrays from Aim 1 and Arabidopsis defense-related mutants to define the expression signatures resulting from the activation of defense pathways. 3) Create a web-accessible plant-microbe interaction database (PMIDB). This database, which will be accessible at http://genetics.mgh.harvard.edu/ausubelweb/nsf2010/NSF_2010.html, will be developed during the next four years and will contain standardized experimental procedures for analyzing host defense responses, a list of all the pathogenesis-related mutants and their phenotypes, a list of defense-related genes with links to various sequence databases, and expression profiles of different plant-pathogen interactions and different defense-related mutants. This 2010 Project provides a unique opportunity for applying genomic approaches to genetic analysis of plant defense mechanisms. Understanding the mechanisms of plant defense is of interest not only to basic science but also to development of agriculture and protection of the environment.