Stage-Dependent Callus Induction in Agapanthus praecox: Multi-Omics Reveals the Semi-Mature Pedicel Explant as the Optimal Choice

Callus induction is the foundation for large-scale and rapid plant propagation, and explant age is a key factor affecting callus induction efficiency and in vitro culture outcomes. Pedicels are the main explants for Agapanthus praecox tissue culture. This study analyzed three pedicel developmental stages (S1: immature, S2: semi-mature, S3: mature) and their induced calli (C1, C2, C3). We integrated transcriptomics, metabolomics (LC-MS/GC-MS), quantitative real-time PCR (qRT-PCR), and weighted gene co-expression network analysis (WGCNA) to clarify the physiological and molecular mechanisms of pedicel regenerative potential. Results showed that S2 exhibited the highest callus induction rate, while C2 showed superior proliferation coefficients and regenerative potential. In pedicel samples, differentially expressed genes were significantly enriched in the MAPK signaling pathway and plant hormone signal transduction pathway, while differentially accumulated metabolites were linked to energy metabolism, amino acid/nucleotide metabolism, and stress responses. Key metabolites (e.g., carbohydrates, amino acids, thidiazuron, and β-chlorogenin) played specific roles in maintaining the meristematic capacity of pedicels. qRT-PCR further confirmed that S2 maintained balanced endogenous hormone signaling and proper cell wall modification. Furthermore, WGCNA identified a key module associated with oxidative stress responses along with S2. Overall, the regenerative potential of pedicel is mediated by the balanced hormone signal transduction, metabolic reprogramming, and epigenetic regulation in A. praecox.