Abstract
In plants, virus infection triggers the accumulation of virus-derived small RNAs due to an endogenous host defense mechanism called RNA interference (RNAi). Beet necrotic yellow vein virus (BNYVV) is the causal agent of the economically significant rhizomania disease of sugarbeet. In this study, using high-throughput small RNA sequencing, we analyzed the frequency and distribution of virus-derived small RNAs of BNYVV to explore RNAi-based antiviral strategy for rhizomania disease management. The roots of sugarbeet seedlings were infected with sap obtained from inoculating RNA transcripts of infectious clones of RNA1, RNA2, RNA3, and RNA4 of BNYVV. At three different time points, virus-infected root samples were collected, and high-throughput small RNA sequencing was carried out for each time point along with mock-inoculated control. Mapping of virus-derived small RNAs in both sense- and antisense-orientations to BNYVV genome revealed the frequency and distribution patterns of small RNA in the root tissue of sugarbeet. This study details small RNA hotspots on various RNA segments of the BNYVV genome, which can aid in developing RNAi-based antiviral strategies for managing rhizomania disease.