Advancing Secondary Metabolite Production: Insights into Hairy Root Systems, Meta-Omics Integration, and Process Intensification in Solanaceae

Abstract

By the mid-1980s, in vitro–produced hairy roots became an effective system for studying plant secondary metabolite biosynthesis. Hairy roots are genetically stable, highly reproducible, and grow rapidly on low-cost media without phytohormones, making them suitable for metabolic studies and bioprocessing. Their application has advanced research on gene function, enzyme regulation, and targeted metabolite production. Understanding complex biosynthetic pathways requires integrated metabolite profiling with multi-omics approaches, particularly transcriptomics (RNA sequencing). Such integrative meta-omics frameworks offer valuable insights into metabolite synthesis in medicinal plants. Species of the Solanaceae family are notable for their nutritional and therapeutic importance and their ability to produce diverse bioactive compounds, including alkaloids, flavonoids, glycosides, and terpenoids. This review highlights recent progress in enhancing secondary metabolite production through improved hairy root induction, process intensification, bioreactor optimization, and integrative metabolomics–transcriptomics strategies for identifying species with industrial potential.