Small RNA and degradome deep sequencing reveal regulatory roles of miRNAs in response to Sugarcane mosaic virus infection on two contrasting sugarcane cultivars.

MicroRNAs (miRNAs) play an essential regulatory role in plant-virus interaction. However, few studies have focused on the roles of miRNAs and their targets after Sugarcane mosaic virus (SCMV) infection in sugarcane. To address this issue, we conducted small RNA and degradome sequencing on two contrasting sugarcanes (SCMV-resistant FG1 and susceptible Badila) infected by SCMV at five-time points. A total of 1578 miRNAs were profiled from 30 small RNA libraries, comprising 660 known miRNAs and 380 novel miRNAs. Differential expression analysis of miRNAs revealed that most were highly expressed during the SCMV exponential phase in Badila at 18h post-infection, with expression profiles positively correlated with virus replication dynamics, as observed through clustering. Analysis of degradome data indicated a higher number of differential miRNA targets in Badila compared to FG1 at 18 hours post-infection. Gene ontology (GO) enrichment analysis significantly enriched the stimulus-response pathway, suggesting negative regulatory roles to SCMV resistance. Specifically, miR160 exhibited upregulated expression patterns and validated in Badila through quantitative real-time PCR in the early stages of SCMV multiplication. Our research provides new insights into the dynamic response of plant miRNA and virus replication and contributes valuable information on the intricate interplay between miRNAs and SCMV infection dynamics.