In the near future, the complete sequence of the Arabidopsis genome will be known, which will lead to the identification of nearly all Arabidopsis genes. Most of these genes will have similarity with genes in other plants and many will have unknown function. The overall goal of this project is to provide plant biologists with a set of powerful tools that can be used in their efforts to understand the function and interrelationships of the 20,000 or more genes in this and other plants. The project has three components: technology development, service to the community, and biological application.
Two synergistic technologies to investigate gene function will be developed and provided at service facilities. The first will be to assemble DNA microarrays of the genes of Arabidopsis. By hybridizing these arrays with probes corresponding to mRNA from different tissues and organs of wild type and mutant plants, global gene expression patterns under a variety of conditions can be investigated. Database and software support will facilitate sophisticated searching and comparisons among these global expression patterns. In parallel with the microarray experiments, the second technology development effort will be to optimize screening of Arabidopsis plants for mutations ("gene knockouts"). This will enable establishment of a gene knockout facility. A long-term goal of this facility will be to knock out all the genes of Arabidopsis. The PIs will use their microarrays to speed up the identification of gene knockouts from pools of candidates. The gene knockout facility and the microarray facility will comprise the service component of this project. The community will also be provided access to project databases and boinformatics tools through the existing Arabidopsis thaliana DataBase (AtDB) so that microarray and gene knockout data can be analyzed and cross-referenced with other plant genome data most effectively.
The synergy between the microarray and gene knockout technologies will be most fully realized within the biological application component of this proposal. This component will focus on enhancing understanding of plant-specific genes of unknown function, but it will generate a large amount of data on the other Arabidopsis genes as well. Plant-specific genes (i.e., genes found in Arabidopsis and other plants but not in yeast, bacterial, or animal systems) are of great interest because they may be involved in plant-specific processes such as plant-pathogen interactions, cell-wall biosynthesis, and others. The PIs will identify knockout mutations in a large number of these genes and then examine the mutant plants for altered phenotypes under a variety of conditions. This will allow members of the community to formulate and test hypotheses about the function of these plant-specific genes.
The impact of this project is expected to extend far beyond Arabidopsis. This is particularly true for the information obtained about plant-specific genes, many of which will be of general significance to crop plants and other plants of commercial value.
