title: Transcriptome profiling confirmed correlations between symptoms and transcriptional changes in RDV infected rice and revealed nucleolus as a possible target of RDV manipulation.
abstract: BACKGROUND
  Rice dwarf virus (RDV) is the causal agent of rice dwarf disease, which limits rice production in many areas of south East Asia. Transcriptional changes of rice in response to RDV infection have been characterized by Shimizu et al. and Satoh et al.. Both studies found induction of defense related genes and correlations between transcriptional changes and symptom development in RDV-infected rice. However, the same rice cultivar, namely Nipponbare belonging to the Japonic subspecies of rice was used in both studies.
  
  
  METHODS
  Gene expression changes of the indica subspecies of rice, namely Oryza sativa L. ssp. indica cv Yixiang2292 that show moderate resistance to RDV, in response to RDV infection were characterized using an Affymetrix Rice Genome Array. Differentially expressed genes (DEGs) were classified according to their Gene Ontology (GO) annotation. The effects of transient expression of Pns11 in Nicotiana benthaminana on the expression of nucleolar genes were studied using real-time PCR (RT-PCR).
  
  
  RESULTS
  856 genes involved in defense or other physiological processes were identified to be DEGs, most of which showed up-regulation. Ribosome- and nucleolus related genes were significantly enriched in the DEGs. Representative genes related to nucleolar function exhibited altered expression in N. benthaminana plants transiently expressing Pns11 of RDV.
  
  
  CONCLUSIONS
  Induction of defense related genes is common for rice infected with RDV. There is a co-relation between symptom severity and transcriptional alteration in RDV infected rice. Besides ribosome, RDV may also target nucleolus to manipulate the translation machinery of rice. Given the tight links between nucleolus and ribosome, it is intriguing to speculate that RDV may enhance expression of ribosomal genes by targeting nucleolus through Pns11.
authors.forename: Liang
authors.initials: L
authors.lastname: Yang
authors.forename: Zhenguo
authors.initials: Z
authors.lastname: Du
authors.forename: Feng
authors.initials: F
authors.lastname: Gao
authors.forename: Kangcheng
authors.initials: K
authors.lastname: Wu
authors.forename: Lianhui
authors.initials: L
authors.lastname: Xie
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China. wuzujian@126.com.
authors.forename: Zujian
authors.initials: Z
authors.lastname: Wu
authors.forename: Jianguo
authors.initials: J
authors.lastname: Wu
mesh_terms: D002466:Cell Nucleolus / Q000821:virology*; D020869:Gene Expression Profiling; D054884:Host-Pathogen Interactions; D046228:Microarray Analysis; D012275:Oryza / Q000235:genetics / Q000276:immunology / Q000821:virology*; D010935:Plant Diseases / Q000276:immunology / Q000821:virology*; D060888:Real-Time Polymerase Chain Reaction; D012087:Reoviridae / Q000276:immunology / Q000502:physiology*