An efficient virus-induced gene silencing of PDS gene in Solanum lycopersicum (cv. Rio Grande) and its functional analysis

Solanum lycopersicum L. is the second most significant fruit crop after potato. It is a rich source of various vitamins, dietary components, and carotenoid content as well. Carotenoids are essential pigments in numerous physiological processes as well as accessory pigments in photosynthesis regulated by phytoene desaturase (PDS) gene. Although the role of PDS gene has been reported in various plants, its role in Pakistan's local cultivar "Rio Grande" has not been investigated yet. Therefore, the current research aimed to evaluate PDS gene's function via TRV-VIGS-based optimized transient silencing protocol. Briefly, PDS gene of tomato was studied computationally for its localization and potential functions. Afterward, the PDS gene was silenced in Rio Grande by agro-infiltration through TRV-VIGS. In order to ensure effective silencing, pigment analysis, PDS gene molecular analysis, and infiltration efficacy were all investigated. Computational studies revealed high conservation in the promoter of PDS gene among selected plant species with a prevalence of CAAT-box and TATA-box. The study highlighted chloroplast to be the principal cellular structure where the majority of PDS protein is found. A transcriptome study of the transiently silenced Rio Grande revealed a considerable reduction in PDS mRNA transcripts in leaves with reference to the respective control. Pigment analysis of the PDS-silenced albino plant leaves showed approximately 90% reduction in their chlorophyll a, chlorophyll b, and carotenoid content suggesting the successful silencing of PDS gene as its active expression plays a positive role in pigment synthesis. The obtained results highlight the role of PDS gene in Rio Grande as well as TRV-based VIGS to be a promising technique to improve crop attributes by efficiently silencing the target genes.