Integrated metabolomics, transcriptional, and physicochemical analysis reveals key metabolites and genes associated with somatic embryogenesis in Phyllostachys pubescens

Phyllostachys pubescens (Moso bamboo) is a significant perennial crop species that provides valuable nutritional and industrial uses, as well as carbon sequestration. Due to its remarkable growth rate, bamboo offers an ideal system for studying organogenesis, particularly in monocots. Somatic embryogenesis (SE) serves as a useful technique for crop breeding and improvement. SE in moso bamboo (Phyllostachys pubescens) remains challenging due to limited knowledge of its transcriptional and metabolomic reprogramming. To address this, we optimized callus initiation (MS + 18.1 µM 2,4-D + 8.5 µM picloram), callus proliferation (MS + 12.5 µM 2,4-D + 8.5 µM picloram), and somatic embryogenesis (MS + 1.1 µM 2,4-D + 3.3 µM metatopolin), using nodal segments as explants. UHPLC-Q-TOF-MS-based metabolite profiling revealed distinct biochemical trajectories across developmental stages of P. pubescens. NEC (non-embryogenic callus) was enriched in flavonoids, alkaloids, and saponins, while in-vitro shoots showed flavonoids and glycosides enrichment, and ex-vitro shoots showed high accumulation of glycosides and terpenoids. In contrast, EC (embryogenic callus) showed elevated levels of fatty acid derivatives (α-ESA, 26-Methyl Nigranoate), phytoalexins (Wyerone acid), sesquiterpene (Alpha-santalal, Beta-guaiene), flavonoid glycosides, and plant hormones (Cis-Zeatin, Gibberellin A45), indicating a metabolically active state supporting somatic embryogenesis. Similarly, genes and transcription factors controlling cell differentiation and embryogenesis were upregulated during SE. This study provides a comprehensive resource to facilitate future genomic and genetic investigations aimed at deciphering the molecular basis of organogenesis and advancing research on somatic embryogenesis in bamboo.