| Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most important world-wide diseases in rice. In the last decade, our understanding of the molecular basis of interactions of Xoo with rice has been advanced by the elucidation of functions of bacterial genes in the pathogenic interactions. Dozens of pathogenicity-related genes have been isolated and characterized from Xoo. However, the interaction relations between rice and Xoo and the pathogenesis mechanisms of Xoo are complex, litter is known about many of virulence and avirulence mechanisms of the pathogen. The scientific basis on development of more innovative, effective and durable strategies for disease control will be provided, while the pathogenic mechanisms of Xoo are well elucidated. The whole genome sequencing of Xoo has provided new opportunities and prospective for researches on Xoo biology on a genome-wide scale. DNA microarray is one of the newly-developed genomic technologies. What makes DNA microarrays especially attractive is the combination of high throughput, parallelism, speed, and automation. The global nature of DNA microarray technique has made it widely used. Using this technique to analyze the pathogen gene expression profile during infection is a promising approach to study pathogenesis mechanisms.In this study, the gene expression profiles of Xoo (JXO I) during different stages of interaction with rice (Oryza sativa subsp. japonica) were investigated using microarray, and many differentially expressed genes were identified. This study provides an innovative approach for research into interactions between Xoo and rice. Similar reports have not yet been seen so far.Firstly, the DNA microarray technology platforms were established. The local genome databases were developed based on the sequences of recently finished Xoo genome and some of other related bacterial genomes. Some genes of Xoo were selected as the candidate genes used in the DNA microarray development, including the pathogenicity genes, species-specific genes, regulator genes and conserved genes in phytopathogenic bacteria. DNA microarrays carrying Xoo DNA segments representing 371 ORFs were successfully constructed. The DNA microarray manufacturing processes have been optimized.Secondly, an in vitro system was established to mimic the early stage of Xoo infection in rice. Thesystem was successfully used to analyze the Xoo gene expression profiling during the early stage of infection. Results showed that 50 genes of Xoo were up-regulated and 6 genes were down-regulated 15 min post contact with detached rice leaf tissues.Thirdly, the ways was found out to analyze the in vivo gene expression profiling of Xoo. The gene expression profile of Xoo 7d and lOd post-inoculation were analyzed. Results showed that 38 genes were up-regulated and 29 genes were down-regulated 7d post-inoculation;76 genes up-regulated and 9 genes down-regulated 10 d post-inoculation.Fourthly, the genome-directed primers (GDPs) were designed and synthesized based on the Xoo genome sequence. The GDPs were used to analyze the in vivo gene expression profile of Xoo Id, 3d and 7d post-inoculation. Results showed that 43 genes were up-regulated and 35 genes were down-regulated Id post-inoculation;73 genes up-regulated and 37 genes down-regulated 3 d post-inoculation;54 genes up-regulated and 24 genes down-regulated 7 d post-inoculation.In this study, some gene expression dynamics were obtained by analyzing the gene expression profiles of during the different stages of interactions with rice. Some of the new candidate bacterial genes related to pathogenesis were identified. The DNA microarray technology platforms and systems were developed to study infectome of phytopathogenic bacteria. These results provide the solid foundations for the further functional genomic analysis towards pathogenicity of Xoo and other phytopathogenic bacteria.
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