Optimization of In Vitro Organogenesis and Phenolic Production in Physalis peruviana L. Through Explant Type and Auxin–TDZ Interactions

P. peruviana is a species of agronomic and biotechnological interest; however, the relationship between in vitro regeneration and phenolic compound production remains poorly explored. This study evaluated the combined effects of thidiazuron (TDZ), explant type (cotyledon and hypocotyl), auxin type (naphthaleneacetic acid, NAA, or indole-3-butyric acid, IBA), and auxin concentration on shoot organogenesis, photosynthetic pigment content, and phenolic accumulation. An initial screening identified 4.54 µM TDZ as the optimal concentration for shoot induction. Subsequent experiments showed that morphogenic and physiological responses were strongly dependent on the interaction among explant type, auxin type, and auxin dose. Cotyledon explants consistently exhibited higher shoot regeneration, vigor, biomass accumulation, and photosynthetic pigment content than hypocotyl explants, which showed reduced physiological performance and a higher tendency for callus formation. NAA-based treatments primarily enhanced morphogenic traits, whereas IBA-based treatments were associated with increased photosynthetic pigment content and phenolic accumulation. Multivariate analysis integrating morphogenic, physiological, and biochemical variables identified cotyledon explants cultured with 0.5 µM IBA in the presence of 4.54 µM TDZ as the treatment achieving the most favorable balance between shoot regeneration, physiological stability, and controlled phenolic accumulation. These findings provide a robust basis for optimizing in vitro culture systems of P. peruviana that balance growth, physiological integrity, and secondary metabolism.