Post-transcriptional and Epigenetic Arms of RNA Silencing: A Defense Machinery of Naturally Tolerant Tomato Plant Against Tomato Leaf Curl New Delhi Virus

Tomato leaf curl disease (ToLCD), caused by strains of Tomato leaf curl virus, is major constraint to tomato production globally. The present study was aimed to understand the mechanisms of ToLCD tolerance in a naturally tolerant tomato cultivar through post-transcriptional and DNA methylation-specific RNA silencing. We evaluated the distribution of virus-derived short-interfering RNAs (siRNAs) throughout the Tomato leaf curl New Delhi virus (ToLCNDV) genome along with DNA methylation patterns in intergenic (IR) and Rep (AC1) regions in two tomato cultivars differing in their ToLCNDV tolerance. The methylation pattern was correlated by expression analysis of key methyltransferases genes. In the tolerant cultivar, higher accumulation of viral IR-specific 24-nucleotides (nt) siRNA and AC1-specific 21-nt siRNA were found. Higher methylation levels were observed in various regions of IR. Additionally, AC1 region which facilitates binding of plant nuclear proteins was hypermethylated. DNA methylation in the key regulating region may control the expression of AC1, AC2, and AC3 genes. Components of RNA silencing and DNA methylation machinery were found to be differentially expressed in both the cultivar of tomato at 21 dpi. Thus, we infer that both viral DNA methylation and siRNA-mediated RNA degradation play an important role in conferring tolerance against Tomato leaf curl New Delhi virus. Due to the inability to achieve field resistance in transgenic tomato by deploying the viral genes, targeting the viral genomic regions through RNAi technology reported here could offer an alternate defense strategy for generating transgenics to prevent yield loss.