Metabolo-Transcriptomic Analysis Reveals the Mechanisms Underlying Seed Dormancy Release in Polygonatum sibiricum

The seeds of Polygonatum sibiricum exhibit dormancy, which poses a major challenge for its cultivation. To elucidate the regulatory mechanisms underlying dormancy release, we performed integrated transcriptomic and metabolomic analyses on seeds at 0, 5, 10, and 15 d after seed imbibition. Physiological assays revealed progressive declines in abscisic acid (ABA) and starch levels, alongside increases in gibberellin (GA) and soluble sugar contents, reflecting the metabolic changes accompanying the transition from dormancy to germination. Transcriptomic analysis identified 11,520 expressed genes, with 6753, 7775 and 9387 differentially expressed genes (DEGs) at T5, T10, and T15, respectively. KEGG enrichment highlighted starch and sucrose metabolism and plant hormone signal transduction as key pathways. Notably, the GA biosynthesis gene GA3ox was markedly upregulated, while the DELLA repressor (Isoform0012761) showed sustained downregulation, suggesting relieved GA signaling. In the ABA pathway, CYP707A catabolic genes exhibited biphasic expression, and ABA signaling components (PYL, PP2C, SnRK2) showed stage-specific remodeling. A total of 316, 412, and 479 differentially expressed transcription factors were identified across stages, with the GRAS family being the largest. Co-expression network analysis revealed 19 transcription factors integrating starch/sucrose metabolism with ABA and GA signaling, most of which were downregulated, except one C2H2 member showing sustained upregulation. These findings demonstrate that dormancy release in P. sibiricum is governed by coordinated hormonal reprogramming, metabolic mobilization, and transcription factor-mediated regulation, providing a theoretical foundation for improving seed germination in this medicinal plant.