Light Spectrum and Explant Type Drive Hormonal and Proteomic Reprogramming in Micropropagation of the Endangered Paubrasilia echinata

Paubrasilia echinata , the national tree of Brazil, is critically endangered due to centuries of overexploitation for its high-quality wood and dye-producing sap. Consequently, the development of efficient propagation systems is urgent for its conservation and restoration. In vitro culture represents a viable alternative to conventional propagation, enabling large-scale plantlet production and the preservation of elite genotypes. This study aimed to evaluate the effects of explant type, cytokinin, and light spectrum on in vitro shoot development, alongside changes in polyamine (PA) and plant hormone profiles, and to assess the impact of indole-3-butyric acid (IBA) on ex vitro rooting. This is the first integrated analysis combining explant type, light quality, and physiological–proteomic responses during in vitro development of P. echinata . Cotyledonary nodal segments produced longer shoots than apical nodal explants. The red–blue enriched LED W/mB/dR/fR lamp markedly improved shoot elongation, biomass accumulation, and endogenous levels of BA and putrescine. Proteomic analysis revealed increased accumulation of proteins related to photosynthesis, antioxidant defense (APX, PODs), cytoskeleton organization (tubulin), and stress tolerance (HSPs), indicating enhanced cellular homeostasis and photomorphogenic responses. Ex vitro rooting ranged from 50–65% and was not significantly influenced by explant type or IBA concentration. Overall, these findings establish a physiologically supported micropropagation protocol for large-scale production of P. echinata , providing a strategic tool for the conservation of this culturally and ecologically emblematic Brazilian species.