BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease in most of the rice growing regions worldwide. Xoo injects the transcriptional activator-like (TAL) effector protein into the host cell to induce the susceptibility (S) gene(s) for spreading the disease. In the current study, a susceptible rice genotype, JG30, was inoculated with wild Xoo strain PXO99A and its mutant PH without any TAL effector, to retrieve the differentially expressed genes (DEGs) having a role in susceptibility. RESULTS RNA-Seq data analysis showed that 1143 genes were significantly differentially expressed (p-value ≤0.05) at 12, 24, 36 and 48 h post inoculation (hpi). Expression patterns, evaluated by quantitative real-time PCR (qRT-PCR), of randomly selected eight genes were similar to the RNA-Seq data. KEGG pathway classified the DEGs into photosynthesis and biosynthesis of phenylpropanoid pathway. Gene ontology (GO) analysis categorized the DEGs into the biological pathway, cellular component, and molecular function. We identified 43 differentially expressed transcription factors (TFs) belonging to different families. Also, clusters of the DEGs representing kinase and peroxidase responsive genes were retrieved. MapMan pathway analysis representing the expression pattern of genes expressed highly in biotic stress and metabolic pathways after PXO99A infection relative to PH. CONCLUSIONS DEGs were identified in susceptible rice genotype inoculated with PXO99A relative to mutant strain PH. The identified 1143 DEGs were predicted to be included in the different biological processes, signaling mechanism and metabolic pathways. The Jasmonic acid (JA) responsive genes were identified to be downregulated in PXO99A infected leaves. This study would be useful for the researchers to reveal the potential functions of genes involved in the rice susceptibility to PXO99A infection.

中文翻译：

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水稻黄单胞菌PV触发的基因表达变化的RNA-Seq分析。水稻基因型易感的米粉。

背景Xanthomonas oryzae pv。稻米（Xoo）在全世界大多数稻米种植地区都是一种破坏性疾病。Xoo将转录激活因子（TAL）效应蛋白注射到宿主细胞中，以诱导易感性（S）基因传播疾病。在当前的研究中，用野生Xoo菌株PXO99A及其突变体PH接种了不敏感的水稻基因型JG30，该突变体PH没有任何TAL效应子，以检索在易感性中起作用的差异表达基因（DEG）。结果RNA-Seq数据分析显示，在接种后（hpi）12、24、36和48 h，1143个基因显着差异表达（p值≤0.05）。通过定量实时PCR（qRT-PCR）评估的随机选择的八个基因的表达模式与RNA-Seq数据相似。KEGG途径将DEGs分为苯丙烷途径的光合作用和生物合成。基因本体论（GO）分析将DEG分为生物途径，细胞成分和分子功能。我们确定了43个差异表达的转录因子（TFs），属于不同的家族。同样，检索到代表激酶和过氧化物酶响应基因的DEG簇。MapMan途径分析代表了相对于PH感染PXO99A后在生物应激和代谢途径中高表达的基因的表达模式。结论相对于突变菌株PH，在接种PXO99A的易感水稻基因型中鉴定到DEG。预计已鉴定出的1143个DEG包含在不同的生物过程，信号传导机制和代谢途径中。已确定茉莉酸（JA）响应基因在PXO99A感染的叶子中被下调。这项研究对于研究人员揭示与水稻对PXO99A感染易感性有关的基因的潜在功能将是有用的。