Comparative analysis of disease resistance related genes in rice

Rice provides staple food for over half of the world's population. In respect that pathogen-induced diseases represented by fungal blast ( Magnaporthe grisea) and bacterial blight (Xanthomonas oryzae pv. oryzae) have heavy impact on rice production in China and in other rice growing countries, and rice itself is a model plant for functional genomic study, the long-term goal of this research is to delineate the disease resistance related genes and their regulations in rice defense mechanisms and to harness this knowledge to improve disease resistance in crops.; To test the hypothesis that in the race specific resistance mediated by different resistance (R) genes, the components of disease resistance signaling pathways downstream of R genes may contribute to the resistance spectra, large-scale gene expression profiling were performed by using cDNA microarray technology to do comparative analysis of rice near isogenic lines carrying different R genes and exhibiting different resistant spectra to rice bacterial blight and blast diseases.; In the study, cDNA microarray technology was successfully set up. Two sets of rice cDNA microarrays were constructed, one containing over 10,000 cDNA clones from a rice line inoculated with incompatible blast pathogens (Pi Chip) and the other containing over 9,000 cDNA clones from 14 subtraction libraries made from nine rice lines after blight bacteria inoculation (Xa Chip).; Statistical analysis of microarray data identified a group of classifier genes whose expression profile can be used to distinguish resistant (R) versus sensitive (S) phenotypes toward rice diseases. Hierarchical clustering demonstrated the relationship between gene expression profiles and the resistant spectra. In addition to the clustering analysis frequently used in plant cDNA microarray analysis, the class prediction analyses technique which used in human disease research were adopted to the study of plant disease resistance related phenotypes. The combined effort of unsupervised and supervised comparison methods reveals the correlation between gene expression profiles and resistance phenotypes or even resistance spectra. This provides support to the notion that global transcriptional re-programming is an important strategy for disease resistance and different signal transduction pathways may lead to distinct patterns of gene expression.; Comparative gene expression analyses identified hundreds of rice disease resistance correlation genes, which shed light on the disease resistance mechanisms in rice and enriched the gene pool for engineering rice disease resistance. Some genes never identified in previous studies of plant disease resistance were found in the research. Quantitative PCR was employed to confirm the microarray data and to perform kinetic expression analyses of selected candidate defense signaling regulator genes. The promising results achieved by rapid functional test of these genes in transgenic Arabidopsis proved the value of the microarray analysis in identification of disease resistance regulators in rice.