Multi-omics analysis of carbon metabolism dynamics and its molecular mechanisms during rice seed imbibition and germination

The transition from a dormant reserve to active growth in the plant life cycle is marked by seed germination. Germination efficiency, seedling establishment vigor, and subsequent crop productivity are directly determined by the efficient mobilization and transformation of carbon (C) metabolism. This study used Huhanxiangruan61 (HHXR61) seeds and applied integrated multi-omics technologies including targeted metabolomics, transcriptomics, and enzyme activity assays to systematically investigate C metabolism dynamics and molecular regulatory mechanisms during rice seed imbibition germination at 0 h (CK), 12 h (T1), 24 h (T2) and 48 h (T3). The results indicated that initial starch hydrolysis, mediated by β-amylase (β-AL), occurred during the early germination period (0–12 h), thereby providing a primary C source for seed germination. During the middle period (12–24 h), activities of sucrose synthase I (SS-I) and soluble acid invertase (S-AI) key enzymes in sucrose metabolism increased alternately, driving sucrose decomposition into glucose and fructose, whereas α-amylase (α-AL) and starch debranching enzyme (DBE) activities also rose, further accelerating starch hydrolysis. In the later stage (24–48 h), activities of fructokinase (FRK), hexokinase (HK), phosphofructokinase (PFK), and pyruvate kinase (PK) increased synchronously, promoting pyruvate production and significantly enhancing the metabolic flux of glycolysis/gluconeogenesis and the tricarboxylic acid (TCA) cycle. C metabolic homeostasis was maintained by glucose-6-phosphatase (G6P) and trehalose-6-phosphate synthase (TPS) through regulation of metabolite flux. KEGG metabolic pathway enrichment analysis revealed that starch and sucrose metabolism, glycolysis/gluconeogenesis, and the pentose phosphate pathway were the most enriched pathways during germination. Integration with transcriptomic data revealed that the genes encoding the aforementioned enzymes exhibited synchronous expression at each time point, forming a defined “gene-enzyme-metabolite” regulatory network. The study elucidated the dynamic succession of C metabolic pathways during rice seed germination.