Systemic metabolic reprogramming underlies cold stratification-induced seed dormancy release in Cercis chinensis...

Cercis chinensis, a woody species with ornamental, medicinal, and potential industrial value, exhibits pronounced seed dormancy that severely constrains propagation efficiency and resource utilization. However, the physiological dynamics and molecular regulatory mechanisms underlying dormancy release remain insufficiently understood. Here, we combined physiological assessments with integrated transcriptomic and proteomic analyses to systematically elucidate the processes governing dormancy release during cold stratification. Cold stratification markedly enhanced germination performance, as reflected by progressive increases in germination percentage and germination index, accompanied by a gradual decline in viability of non-germinated seeds. This process was associated with substantial reconfiguration of seed reserve metabolism, including increased soluble sugar accumulation, depletion of starch and lipid reserves, and dynamic changes in soluble protein content. Enzymatic activities related to starch degradation and central carbon metabolism were significantly modulated, indicating enhanced carbon mobilization and metabolic activation. Concurrently, endogenous phytohormone homeostasis was reprogrammed, characterized by a sustained decrease in ABA and pronounced increases in GA, IAA, and JA. Principal component analysis of physiological traits identified stratification at 0 and 45 days as representative stages of dormancy and dormancy release, respectively, guiding subsequent multi-omics profiling. Integrated transcriptomic and proteomic analyses revealed extensive differentially expressed genes and corresponding proteins enriched in pathways associated with carbohydrate metabolism, hormone biosynthesis and signaling, and energy metabolism. These included starch and sucrose metabolism, glycolysis/gluconeogenesis, the pentose phosphate pathway, fatty acid degradation, the citrate cycle, peroxisome function, and oxidative phosphorylation. Reverse transcription quantitative PCR (RT‑qPCR) validation of selected key genes confirmed the expression trends observed in transcriptome sequencing, demonstrating the reliability of the transcriptomic data. Collectively, our findings demonstrate that dormancy release in C. chinensis seeds represents a systemic transition from metabolic quiescence to metabolic activation, driven by coordinated carbon reserve mobilization, hormonal rebalancing, and enhanced respiratory metabolism. This study provides a comprehensive framework for understanding dormancy regulation in woody plant seeds and offers theoretical support for improving germination efficiency and resource utilization in C. chinensis.