Abstract: 【Objective】To provide theoretical basis for studying the molecular mechanism of the rice to defense against Xanthomonas oryzae pv. oryae(Xoo)and breeding rice varieties resistant to Xoo, the transcriptome of rice infected by Xoo at different time points and the expression of genes related to the infection process were analyzed.【Method】 CBB23,a resistant rice line carrying Xa23 gene,was inoculated with a highly pathogenic wild-type strain Xoo N3-1 by infiltration using sterile needleless syringes. Total RNA of the samples at 0,48 and 72 h post-inoculation was extracted for transcriptome sequencing(RNA-Seq),respectively. Differentially expressed genes(DEGs)were identified,taking|log₂ Fold Change| ≥ 1 and false discovery rate (FDR) <0.01 as the screening criteria. Gene ontology(GO)analysis for functional annotation and KEGG pathway analysis were performed. The reliability of RNA-Seq results was verified by realtime fluorescence quantitative PCR(qRT-PCR).【Result】 About 54.63 Gb of Clean data were obtained from the transcriptome sequencing of a total of 9 samples,and the Clean data of each sample was about 6.07 Gb. The percentage of Q30 base was 94.34% or above. Compared with the control group at 0 h,2361 and 2117 DEGs were identified at 48 and 72 h post-inoculation respectively. Among them,1650 up-regulated genes and 711 down-regulated genes were identified at 48 h,and 1440 up-regulated genes and 677 down-regulated genes were identified at 72 h. GO enrichment analysis results showed that DEGs in response to Xoo infection were significantly enriched in amino acid metabolism and diterpenoid biosynthesis. KEGG metabolic pathway enrichment analysis results showed that the DEGs were mainly enriched in phenylalanine biosynthesis and phenylpropanoid synthesis. DEGs analysis showed that the expression of OsSWEET14 gene in SWEET gene family greatly increased while rice bacterial blight resistant gene Xa23 did not expressed post-inoculation. WRKY transcription factors analysis revealed that the expression of WRKY transcription factors involving in resistance against Xoo decreased. The expression of calcium-dependent protein kinase(CDPK)increased greatly,and the expression of mitogen-activated kinase(MAPK)did not change. The results of gene expression detection by qRT-PCR were consistent with the results of RNA-Seq.【Conclusion】The expression of a large number of amino acid and secondary metabolites such as diterpenoids and flavonoids related genes of rice CBB23 greatly increase in the process of resisting against bacterial pathogen N3-1 infection. The expression of susceptible gene OsSWEET14 increases during the infection process,which may be one of the key susceptible genes regulated. The expression of transcription factors related to disease resistance includes up-regulation and down-regulation. These results indicate that the complex transcriptional regulatory network changes occurr in rice in response to pathogen infection,and the whole disease resistance process is regulated through signal transmission between signaling pathways.