Identification and validation of TFs and lncRNAs in response to Tomato Leaf Curl Bangalore Virus (ToLCBaV) infection in tomato (Solanum spp.)

Tomato leaf curl Bangalore virus (ToLCBaV), often a woeful reason for complete failure of tomato crop in southern India. The plant response to virus infection is a complicated network involving several defence routes. Every defence route involves transcription factors (TFs) and other regulatory transcripts including lncRNA as important regulators of gene expression. These regulators act as both pro-viral and anti-viral factors involved in modulating disease symptoms. This study has reported and validated several TFs and lncRNAs from transcriptome study of tomato lines, IIHR2611 (R) and IIHR 2843 (S) in response to virus infection. Validation was done based on expression analysis of selected TFs and lncRNAs using qPCR at different intervals of ToLCBaV infection. TFs, DREB protein 1A (3.53 folds) and Protein RADIALIS-like 3 (5.27 folds) were induced in R plants upon ToLCBaV infection. Whereas, WRKY TF-53 was upregulated in S (3.36 folds) and down regulated in R (− 3.80 folds) plants upon virus infection. Four lncRNAs were found differentially expressed among R and S lines when analysed using qPCR. The differential temporal gene expression of TFs among S and R plants in response to ToLCBaV infection regulate the resistance or susceptibility. Further studies on the mechanism of resistance of TFs and lncRNAs will aid in unravelling novel antiviral defence pathways in tomato. These findings provide a basis for developing molecular markers for marker-assisted selection and targets for genome editing, paving the way for breeding durable ToLCBaV-resistant tomato cultivars. Understanding the role of TFs and lncRNAs in host-virus interactions could also help address viral infections in other crop species.