Magbanua Zenaida V, Arick Mark, Buza Teresia, Hsu Chuan-Yu, Showmaker Kurt C, Chouvarine Philippe, Deng Peng, Peterson Daniel G, Lu Shien
Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762, USA.
BMC Genomics. 2014 Sep 3;15(1):755. doi: 10.1186/1471-2164-15-755.
Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a model for rice resistance to the disease.
Using inoculated young seedlings as sample tissues, we identified unique transcripts involved with resistance to bacterial panicle blight, including a PIF-like ORF1 and verified differential expression of some selected genes using qRT-PCR. These transcripts, which include resistance genes of the NBS-LRR type, kinases, transcription factors, transporters and expressed proteins with functions that are not known, have not been reported in other pathosystems including rice blast or bacterial blight. Further, functional annotation analysis reveals enrichment of defense response and programmed cell death (biological processes); ATP and protein binding (molecular functions); and mitochondrion-related (cell component) transcripts in the resistant interaction.
Taken together, we formulated a model for rice resistance to bacterial panicle blight that involves an activation of previously unknown resistance genes and their activation partners upon challenge with B. glumae. Other interesting findings are that 1) though these resistance transcripts were up-regulated upon inoculation in the resistant interaction, some of them were already expressed in the water-inoculated control from the resistant genotype, but not in the water- and bacterium-inoculated samples from the susceptible genotype; 2) rice may have co-opted an ORF that was previously a part of a transposable element to aid in the resistance mechanism; and 3) resistance may have existed immediately prior to rice domestication.
由成团泛菌引起的细菌性穗枯病是美国水稻中一种新出现的病害。关于这种病害、病害循环或任何抗病源，人们了解得并不多。为了了解水稻与成团泛菌之间的相互作用，我们通过下一代测序（RNA测序）和生物信息学使用转录组学来鉴定抗性和感病相互作用之间差异表达的转录本，并构建水稻对该病害的抗性模型。
以接种的幼苗作为样本组织，我们鉴定出了与细菌性穗枯病抗性相关的独特转录本，包括一个类PIF的开放阅读框1，并使用qRT-PCR验证了一些选定基因的差异表达。这些转录本包括NBS-LRR类型的抗性基因、激酶、转录因子、转运蛋白以及功能未知的表达蛋白，在包括稻瘟病或白叶枯病在内的其他病理系统中尚未见报道。此外，功能注释分析显示，在抗性相互作用中，防御反应和程序性细胞死亡（生物学过程）、ATP和蛋白质结合（分子功能）以及线粒体相关（细胞成分）转录本富集。
综上所述，我们构建了一个水稻对细菌性穗枯病的抗性模型，该模型涉及在受到成团泛菌攻击时激活先前未知的抗性基因及其激活伙伴。其他有趣的发现是：1）尽管这些抗性转录本在抗性相互作用中接种后上调，但其中一些在抗性基因型的水接种对照中已经表达，而在感病基因型水接种和细菌接种的样本中未表达；2）水稻可能采用了一个以前是转座子一部分的开放阅读框来辅助抗性机制；3）抗性可能在水稻驯化之前就已存在。
