Expression profiling of rice genes in early defense responses to blast and bacterial blight pathogens using cDNA microarray

In order to understand the defense machinery in the model cereal crop rice, we performed a large-scale analysis of rice gene expression in response to rice blast Magnaporthe grisea (M. grisea) or Magnaporthe oryzae and bacterial blight Xanthomonas oryzae pv. oryzae (Xoo) during the early incompatible and compatible interactions. Using a gene chip containing 10 254 rice cDNAs representing 9240 unique genes, we identified 794 and 612 genes differentially expressed in the incompatible and compatible rice–M. grisea interactions, respectively, with 274 genes co-regulated during both interactions. In the rice–Xoo pathosystem, 454 and 498 differentially expressed genes were identified in the incompatible and compatible interactions, respectively, including 237 co-regulated genes in the both interactions. By clustering differentially regulated genes from all these interactions, we identified 29 co-regulated genes in the all four interactions, and 86 and 74 co-regulated genes in the two incompatible and two compatible interactions, respectively. These differentially expressed genes could be classified into three categories, including M. grisea- and Xoo-regulated, M. grisea-specific, and Xoo-specific. The expression patterns of representative defense-related genes were further confirmed by RT-PCR. The large-scale expression data from our microarray analysis indicated the existence of distinctive as well as shared defense pathways between the rice–M. grisea and rice–Xoo interactions.