Omics based approaches to decipher the leaf ionome, transcriptional and mutation changes in Solanum lycopersicum L. crop upon Tomato Brown Rugose Fruit Virus (ToBRFV) infection

Leaf ionomics and transcriptomics approaches can help decipher the interaction between elemental composition and gene expression to understand plant physiology, growth, and responses to various stimuli. In this study, we use an omics-based approach that integrates leaf ionomics and transcriptomics to investigate the changes in the nutritional composition and gene expression profile upon the Tomato Brown Rugose Fruit Virus (ToBRFV) infection in tomato (Solanum lycopersicum L.). Ionomics was used to quantify the nutrient uptake and composition of trace elements, showcasing that the resistant group had significantly higher contents of iron (p-value = 0.039) and nickel (p-value = 0.042) than the susceptible. To identify the key genes regulating the defence mechanisms in plants, transcriptomics analysis was applied revealing the role of iron homeostasis and abscisic acid pathways that could be responsible for conferring resistance against the pathogen. Upon further integration of these differentially expressed genes, a panel of mutation profile was discovered with three important genes - Solyc02g068590.3.1 (K+ transporter), Solyc01g111890.3.1 (LRR), and Solyc02g061770.4.1 (Chitinase) showing a persistent missense mutation. We ascertain the role of these genes and establish their association with plant resistance using genotyping assays in various tomato lines. The targeted selection of these genetic determinants can further assist in enhancing plant breeding and crop yield management strategies.