Transcriptome analysis reveals different response of resistant and susceptible rice varieties to rice stripe virus infection

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.