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Journal of Integrative Agriculture  2023, Vol. 22 Issue (6): 1750-1762    DOI: 10.1016/j.jia.2022.10.010
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Transcriptome analysis reveals different response of resistant and susceptible rice varieties to rice stripe virus infection

LIU Yu1, 2, LIU Wen-wen1, LI Li1, Frederic FRANCIS2#, WANG Xi-feng1#

1 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China

2 Functional & Evolutionary Entomology, Gembloux Agro-BioTech, University of Liège, Gembloux 5030, Belgium

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水稻条纹叶枯病是由灰飞虱(Laodelphax striatellus Fallen)传播的水稻条纹病毒(rice stripe virus, RSV)侵染所致,因其危害性严重被称为水稻的癌症目前,关于RSV侵染后,水稻品种之间的分子差异以及水稻与RSV之间的相互作用的研究仍然不够充分本文利用转录组测序技术(RNA-sequencing, RNA-Seq)分析了在RSV侵染后不同抗性水平水稻品种在转录水平上的差异。通过GOGene Ontology)注释鉴定到了抗、感品种在接种后2天、10天和20天后与转录因子(transcription factor, TF)、过氧化物酶(peoxidase)和激酶(kinase关的差异表达基因。结果表明:抗病品种中与这三类蛋白相关的差异表达基因虽然数量上比感病品种要少,但经显著性分析,在| log2(FoldChange) | > 0 & padj < 0.05的条件下,表达量呈现显著上调或下调表达趋势。通过KEGG(Kyoto Encyclopedia of Genes and Genomes)分析鉴定出参与抗病反应途径的差异基因,包括植物激素信号转导和植物-病原体相互作用。结果表明涉及植物激素信号转导,脱落酸(abscisic acid, ABA)负调控的抗性反应和油菜素内酯(brassinosteroids, BR)正调控的抗性反应在抗、感品种间无差异,但涉及水杨酸(salicylic acid, SA)介导和茉莉酸(jasmonic acid, JA/乙烯(ethylene, ET)介导的抗性反应有所不同。抗、感品种在三个时间节点的差异表达基因在病原相关分子模式激发的免疫反应(PAMP-triggered immunity, PTI)和效应蛋白激发的免疫反应(Effector-triggered immunity, ETI)都存在,但感病品种的特有基因大多涉及PTI,而抗病品种涉及ETI的特有基因数量更多。以上结果揭示了RSV侵染后抗、感品种在转录水平上的差异,为阐明了水稻与RSV互作的机制奠定了基础。


Rice stripe disease, caused by rice stripe virus (RSV) which is transmitted by small brown planthopper (SBPH, Laodelphax striatellus Fallen), resulted in serious losses to rice production during the last 2 decades.  Research on the molecular differences between resistant and susceptible rice varieties and the interaction between rice and RSV remains inadequate.  In this study, RNA-Seq was used to analyze the transcriptomic differences between the resistant and susceptible rice varieties at different times post RSV infection.  Through Gene Ontology (GO) annotation, the differentially expressed genes (DEGs) related to transcription factors, peroxidases, and kinases of 2 varieties at 3 time points were identified.  Comparing these 2 varieties, the DEGs associated with these 3 GOs were numerically less in the resistant variety than in the susceptible variety, but the expression showed a significant up- or down-regulation trend under the conditions of |log2(Fold change)|>0 & Padj<0.05 by significance analysis.  Then through Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, DEGs involved in some pathways that have a contribution to disease resistance including plant hormone signal transduction and plant–pathogen interaction were found.  The results showed that resistance responses regulated by abscisic acid (ABA) and brassinosteroids (BR) were the same for 2 varieties, but that mediated by salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET) were different.  The DEGs in resistant and susceptible varieties at the 3 time points were identified in both PAMP-triggered immunity (PTI) and Effector protein-triggered immunity (ETI), with that most of the unigenes of the susceptible variety were involved in PTI, whereas most of the unigenes of the resistant variety were involved in ETI.  These results revealed the different responses of resistant and susceptible varieties in the transcription level to RSV infection.

Keywords:  transcriptomics       resistance        susceptibility        rice stripe virus (RSV)        infection  
Received: 06 June 2022   Online: 13 October 2022   Accepted: 09 September 2022

This research was supported by the National Key Research and Development Plan of China (2019YFE0108500).

About author:  LIU Yu, E-mail:; #Correspondence WANG Xi-feng, E-mail:; Frederic FRANCIS, E-mail:

Cite this article: 

LIU Yu, LIU Wen-wen, LI Li, Frederic FRANCIS, WANG Xi-feng. 2023. Transcriptome analysis reveals different response of resistant and susceptible rice varieties to rice stripe virus infection. Journal of Integrative Agriculture, 22(6): 1750-1762.

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