State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China.
PLoS One. 2010 Jan 8;5(1):e8632. doi: 10.1371/journal.pone.0008632.
Rice is a very important food staple that feeds more than half the world's population. Two major Asian cultivated rice (Oryza sativa L.) subspecies, japonica and indica, show significant phenotypic variation in their stress responses. However, the molecular mechanisms underlying this phenotypic variation are still largely unknown. A common link among different stresses is that they produce an oxidative burst and result in an increase of reactive oxygen species (ROS). In this study, methyl viologen (MV) as a ROS agent was applied to investigate the rice oxidative stress response. We observed that 93-11 (indica) seedlings exhibited leaf senescence with severe lesions under MV treatment compared to Nipponbare (japonica). Whole-genome microarray experiments were conducted, and 1,062 probe sets were identified with gene expression level polymorphisms between the two rice cultivars in addition to differential expression under MV treatment, which were assigned as Core Intersectional Probesets (CIPs). These CIPs were analyzed by gene ontology (GO) and highlighted with enrichment GO terms related to toxin and oxidative stress responses as well as other responses. These GO term-enriched genes of the CIPs include glutathine S-transferases (GSTs), P450, plant defense genes, and secondary metabolism related genes such as chalcone synthase (CHS). Further insertion/deletion (InDel) and regulatory element analyses for these identified CIPs suggested that there may be some eQTL hotspots related to oxidative stress in the rice genome, such as GST genes encoded on chromosome 10. In addition, we identified a group of marker genes individuating the japonica and indica subspecies. In summary, we developed a new strategy combining biological experiments and data mining to study the possible molecular mechanism of phenotypic variation during oxidative stress between Nipponbare and 93-11. This study will aid in the analysis of the molecular basis of quantitative traits.
水稻是一种非常重要的主食，养活了世界上一半以上的人口。亚洲两个主要的栽培稻亚种，籼稻和粳稻，在其对胁迫的响应方面表现出显著的表型变异。然而，这种表型变异的分子机制在很大程度上仍然未知。不同胁迫之间的一个共同联系是，它们会产生氧化爆发，并导致活性氧（ROS）的增加。在这项研究中，我们应用了甲基紫精（MV）作为 ROS 试剂来研究水稻的氧化应激反应。我们观察到，与 Nipponbare（粳稻）相比，93-11（籼稻）幼苗在 MV 处理下表现出叶片衰老和严重损伤。进行了全基因组微阵列实验，除了 MV 处理下的差异表达外，还鉴定了两个水稻品种之间基因表达水平多态性的 1062 个探针集，这些探针集被分配为核心交叉探针集（CIPs）。通过基因本体论（GO）对这些 CIPs 进行了分析，并突出了与毒素和氧化应激反应以及其他反应相关的富集 GO 术语。这些 CIP 的 GO 术语富集基因包括谷胱甘肽 S-转移酶（GSTs）、P450、植物防御基因和与次级代谢相关的基因，如查尔酮合酶（CHS）。对这些鉴定的 CIPs 进行插入/缺失（InDel）和调控元件分析表明，水稻基因组中可能存在与氧化应激相关的一些 eQTL 热点，例如 10 号染色体上编码的 GST 基因。此外，我们鉴定了一组区分粳稻和籼稻亚种的标记基因。总之，我们开发了一种新的策略，结合生物实验和数据挖掘来研究 Nipponbare 和 93-11 在氧化应激过程中表型变异的可能分子机制。这项研究将有助于分析数量性状的分子基础。
