Transcriptome profiling confirmed correlations between symptoms and transcriptional changes in RDV infected rice and revealed nucleolus as a possible target of RDV manipulation.

Liang Yang,Jianguo Wu,Lianhui Xie,Zhenguo Du,Yi Li,Feng Gao,Zujian Wu,Kangcheng Wu

doi:10.1186/1743-422x-11-81

Abstract

BackgroundRice 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.MethodsGene 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).Results856 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.ConclusionsInduction 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.

Highlights

Rice dwarf virus (RDV) is the causal agent of rice dwarf disease, which limits rice production in many areas of south East Asia
A set of ribosomal genes have been shown to be up-regulated in Arabidopsis, Nicotiana benthamiana and rice infected with Turnip mosaic virus (TuMV), Plum pox potyvirus (PPV) and Rice stripe virus (RSV), respectively [10,11,12]
Changes of most of these genes are consistent with previous studies carried out using N. benthamiana or Arabidopsis thaliana [4,10,11,35,36,37,38,39]

Summary

Introduction

Rice dwarf virus (RDV) is the causal agent of rice dwarf disease, which limits rice production in many areas of south East Asia. Transcriptional response of plants to virus infection is shown to vary depending on virus species, virus strains and the genetic backgrounds of host plants [6,7,8] It shows a tight link with phenotypes and is useful to reveal how a virus colonizes a host, how a host mounts a defense response against a virus, and how a compatible virus-host interaction results in disease symptoms [6,7,8]. These studies find that some genes may be commonly regulated by different viruses in different host plants [9]. A set of ribosomal genes have been shown to be up-regulated in Arabidopsis, Nicotiana benthamiana and rice infected with Turnip mosaic virus (TuMV), Plum pox potyvirus (PPV) and Rice stripe virus (RSV), respectively [10,11,12]

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Results

Conclusion