title: Gene expression profiles deciphering rice phenotypic variation between Nipponbare (Japonica) and 93-11 (Indica) during oxidative stress.
abstract: 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.
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China.
authors.forename: Fengxia
authors.initials: F
authors.lastname: Liu
authors.forename: Wenying
authors.initials: W
authors.lastname: Xu
authors.forename: Qiang
authors.initials: Q
authors.lastname: Wei
authors.forename: Zhenghai
authors.initials: Z
authors.lastname: Zhang
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Xing
authors.forename: Lubin
authors.initials: L
authors.lastname: Tan
authors.forename: Chao
authors.initials: C
authors.lastname: Di
authors.forename: Dongxia
authors.initials: D
authors.lastname: Yao
authors.forename: Chunchao
authors.initials: C
authors.lastname: Wang
authors.forename: Yuanjun
authors.initials: Y
authors.lastname: Tan
authors.forename: Hong
authors.initials: H
authors.lastname: Yan
authors.forename: Yi
authors.initials: Y
authors.lastname: Ling
authors.forename: Chuanqing
authors.initials: C
authors.lastname: Sun
authors.forename: Yongbiao
authors.initials: Y
authors.lastname: Xue
authors.forename: Zhen
authors.initials: Z
authors.lastname: Su
mesh_terms: D020869:Gene Expression Profiling; D017343:Genes, Plant; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D018384:Oxidative Stress; D012333:RNA, Messenger / Q000235:genetics; D017382:Reactive Oxygen Species / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013045:Species Specificity
chemical_list: D012333:RNA, Messenger; D017382:Reactive Oxygen Species