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

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.

Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance

“… Kwenda et al (2016) genome-wide identified potato lincRNAs and functionally analyzed the mechanism in response to Pectobacterium carotovorum subspecies brasiliense infection. A total of 1342 mRNAs and 22 lncRNAs of rice were identified to be differentially expressed after RBSDV infection ( Zhang et al, 2020 ). An lncRNA of rice, ALEX1, whose expression is highly induced by Xoo infection, can active the JA pathway and promote resistance to bacterial blight ( Yu et al, 2020 ).…”

Transcriptional Landscape of Pathogen-responsive Lncrnas Reveals OS_LNC1812-Induced Disease Resistance by Abscisic Acid Pathway in Rice

“…During RBSDV infection, The up-regulated rice signal transductionassociated genes can improve rice resistance by inducting of the jasmonic acid (JA) pathway and inhibiting the abscisic acid (ABA) pathway [12,13]. Recently reports shown that in addition to resistance genes, non-coding RNAs (ncRNAs) including small ncRNAs and long ncRNAs (lncRNAs) also play an important in rice defense against pathogens [14,15]. Although many works associated with functional characterization of small ncRNAs are reported, the function of lncRNAs in plants is largely unknown.…”

“…In contrast, lncRNAs involved in resistance regulatory mechanisms against pathogens are rarely reported, especially in rice [33,34]. Tianze et al revealed the regulatory network between lncRNA and mRNA in rice response to RBSDV infection by performing RNA-seq [35]. To date, the expression pro le and functional characterization of lncRNAs during RSV and RBSDV infection in rice are still largely unknown.…”

Special Issue: “Plant Virus Pathogenesis and Disease Control”

“…Three groups addressed the roles of non-coding RNAs in plant virus infections [5][6][7]. Liu and colleagues used microarray analysis to screen microRNAs (the microRNAome) and obtained a global profile allowing for the identification of some miRNAs and their roles as well as their corresponding target mRNAs, and resulting defense signaling pathways in beet necrotic yellow vein virus pathogenesis in Nicotiana benthamiana plants [6].…”

“…Suppression of nbe-miR1919c-5p by STTM resulted in increased titers for TbCSV and TbCSB, plus more severe symptoms, including leaf curling in plants. Zhang and colleagues assessed the network of differentially expressed long non-coding RNAs (lncRNAs, >200 nt) and mRNAs in rice plants infected with rice black-streaked dwarf virus (RBSDV) [7]. The biological roles of lncRNAs are largely still unknown.…”