Screening and Functional Characterization of Rice Gene Candidates Affecting Rice Stripe Virus Replication and/or Infection Cycle

Rice stripe virus (RSV) is a single-stranded RNA virus which is one of the most harmful virus of rice in East Asian countries. In infected rice, RSV causes severe symptoms including chlorotic stripes, chlorosis, and necrosis of leaves. MicroRNAs (miRNAs) are small non-coding RNAs, which is consisted of 19-24 nucleotides. It is known that miRNAs regulate gene expression in transcriptional or post-transcriptional manner as a defense mechanism for viral infection. We have conducted RNA-Seq and small RNA sequencing analyses to identify differently expressed rice genes and miRNAs which is induced upon RSV infection in three different time points. From 8 to 11% of rice genes was differently expressed and 374 conserved miRNAs were identified from miRBase database. Among the 374 conserved miRNAs, 19 novel miRNAs were differentially expressed in 3 different time points. Based on result of RNA-Seq and small RNA sequencing data, we selected a total of 23 miRNA target genes as candidate host factors that might affect RSV infection. Furthermore, we selected 9 Arabidopsis gene orthologues in rice which is involved in jasmonic acid (JA) and mitogen-activated protein kinase (MAPK) pathways in Arabidopsis thaliana. To verify possible function(s) of these selected candidate genes, we induced a transient over-expression system with Nicotiana benthamiana in which RSV can replicate and cause visible disease symptoms. This study will provide an efficient method for screening of rice genes involved in RSV infection and for characterizing possible functions of selected rice genes differentially expressed in RSV infection.