Genome-wide identification and association analysis for virus-responsive lncRNAs in rice (Oryza sativa L.)

Long non-coding RNAs (lncRNAs) produced by the plant genome are essential regulators of diverse biological processes. Despite increasing knowledge on the role of lncRNAs in plant development, their action in response to plant disease, especially in rice, is poorly understood. In this study, the comprehensive disease-responding lncRNA profile in rice response to rice black-streaked dwarf virus (RBSDV) and rice stripe virus (RSV) was investigated for the first time. Transcriptomic analysis of rice leaves infected with these two pathogens had identified 1925 lncRNAs, of which 724 were derived from alternative splicing (AS) events. Differentially expression analysis identified 344 and 176 differentially expression lncRNAs (DELs) in RBSDV vs CK and RSV vs CK, respectively. The targets of these DELs mainly associated with multiple immune-related pathways, such as "plant hormone signal transduction," and "phenylpropanoid biosynthesis", and 'plant-pathogen interaction'. For further analyzing the regulatory relationship among transcription factors, lncRNAs, and mRNAs, the gene regulatory network was constructed by performing GENIE3. Finally, a total of 2484 TF-lncRNA-target pairs, including 60 TFs (as regulatory factors), 21 lncRNAs regulated by TFs and targeting mRNAs (as regulatory factors and targets), and 1064 mRNAs (as targets) were obtained, and all transcripts from TF-lncRNA-target pairs were up-regulated in both comparisons. In these transcripts, each lncRNA regulated by corresponding TF can regulate the TF-targeted mRNA, suggesting that TF may regulate the mRNA via the corresponding lncRNA. This study identified lncRNAs related to multiple viruses infection in rice, which provides another layer of candidates that regulate rice and virus interactions.