Development of an oligonucleotide microarray for the rice genome

 www.ricearray.org

Microarray technology permits biologists to concurrently measure the expression levels of thousands of genes in single experiment. Computational tools can be used to extract biologically significant information from gene expression data, assign functions to genes, and identify genetic regulatory networks. Public-sector access to microarrays is critical to ensure that the public's large investment in rice structural genomics is converted to public scientific and economic benefits.

We are working with TIGR and ISU to develop a public platform of core functional genomics resources including a 40,000-element oligonucleotide array that will be useful for analysis of virtually any trait in rice and a microarray expression database linked to rice genome annotation available to the public for data mining. These materials are essential for elucidation of rice signaling networks. By making these resources broadly available, the project will have far-reaching benefits in global rice research.

We have used the rice oligo arrays to rapidly and efficiently classify defense mutants in rice. Ten carefully selected mutant lines that exhibit altered defense responses to two pathogens were profiled before and after fungal (Magnaporthe grisea) and bacterial (Xanthamonas oryzae pv. oryzae, Xoo) infections. Based on their expression patterns, the mutants have been classified into several groups and a set of novel defense-related genes have been identified (http://www.ricedefensemutant.org/microarray/).