RNA interference (RNAi) using non-coding small RNAs i.e. siRNAs and miRNAs are gaining wide attention for the suppression of intracellular viral target mRNA. Small RNA silencing using target sequences from Tomato leaf curl virus genome were designed via transgene derived siRNAs and artificial microRNA (amiRNA) strategies to generate leaf curl resistance in plants. The siRNA generating sequences covering the replicase gene and RNAi suppressor were selected for various strategies like antisense, self complementary inverted repeats, intron spliced hairpin RNAs, and small hairpin RNAs. Potent siRNAs were selected from different region of the viral genome and targeted by modifying pre-miR159 backbone to produce artificial microRNA. Close sequence homology of one of the viral siRNA with tomato miR3 results in off-target. Our study rationalizes the idea of careful selection of viral sequences for efficient and effective silencing of viral genome either by endogenous and exogenous small RNAi silencing pathways, we also discuss the comparative analysis of both the RNAi silencing system.
