Transcriptome Analysis of Rice Reveals the lncRNA-mRNA Regulatory Network in Response to Rice Black-Streaked Dwarf Virus Infection.

Tianze Zhang,Xueping Zhou,Jianxiang Wu,Qian Liang,Shuai Fu,Chenyang Li,Jiban Kumar Kundu

doi:10.3390/v12090951

Abstract

The plant genome can produce long non-coding RNAs (lncRNAs), some of which have been identified as important regulators of gene expression. To better understand the response mechanism of rice plants to Rice black-streaked dwarf virus (RBSDV) infection, we performed a comparative transcriptome analysis between the RBSDV-infected and non-infected rice plants. A total of 1342 mRNAs and 22 lncRNAs were identified to be differentially expressed after RBSDV infection. Most differentially expressed transcripts involved in the plant–pathogen interaction pathway were upregulated after RBSDV infection, indicating the activation of rice defense response by RBSDV. A network of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) was then constructed. In this network, there are 56 plant–pathogen interaction-related DEmRNAs co-expressing with 20 DElncRNAs, suggesting these DElncRNAs and DEmRNAs may play essential roles in rice innate immunity against RBSDV. Moreover, some of the lncRNA–mRNA regulatory relationships were experimentally verified in rice calli by a quick and effective method established in this study. Three DElncRNAs were selected to be tested, and the results indicated that five mRNAs were found to be regulated by them. Together, we give a whole landscape of rice mRNAs and lncRNAs in response to RBSDV infection, and a feasible method to rapidly verify the lncRNA–mRNA regulatory relationship in rice.

Highlights

Rice black-streaked dwarf disease is an important rice disease in China, Japan, and many otherAsian countries and is caused by Rice black-streaked dwarf virus (RBSDV) [1]
Analysis of the DElncRNA and differentially expressed mRNAs (DEmRNAs) co-expression network showed a complicated gene-regulating relationship, and we focused on transcripts related to the plant–pathogen interaction pathway
Earlier studies have suggested that many of the long non-coding RNAs (lncRNAs) and mRNAs may share the common mechanisms of transcription and processing [45]

Summary

Introduction

Asian countries and is caused by Rice black-streaked dwarf virus (RBSDV) [1]. RBSDV can infect maize, wheat, and several species of weeds [2,3,4,5] to cause Maize rough dwarf disease and wheat dark-green dwarf disease [6,7]. Several studies have shown that the expression of mRNAs and microRNAs in rice and maize plants can be affected by RBSDV infection. The expression of rice signal transduction-associated genes can be altered after RBSDV infection, resulting in inhibition of the abscisic acid (ABA) pathway and induction of the jasmonic acid (JA) pathway [11,12]. Many cell wall biosynthesis-related, chloroplast function-related, and disease resistance or stress-related genes were found to be significantly upregulated after RBSDV infection in maize [13]

Methods

Results

Conclusion