PFK1-mediated metabolic shifts facilitate cold stratification-induced dormancy release in Cercis chinensis seeds

Seed dormancy limits the propagation of Cercis chinensis , an important species of medicinal and ecological significance. This study explores the molecular mechanisms underlying dormancy release during cold stratification. By integrating biochemical analyses, we revealed that cold stratification reduced abscisic acid (ABA) while increasing gibberellin A₃ (GA₃), indole-3-acetic acid (IAA), and jasmonic acid (JA), accompanied by enhanced enzyme activities and shifts in storage substances. Transcriptomic profiling identified 694 genes involved in hormone signaling, DNA replication, and carbon metabolism. Notably, the downregulation of phosphofructokinase1 ( PFK1 ) redirected carbon flux to the pentose phosphate pathway (PPP), meeting the demands for nucleotide precursor and antioxidants. This metabolic shift is critical for breaking non-deep physiological dormancy of C. chinensis seeds. Our findings reveal novel insights into the molecular and metabolic processes driving dormancy release in C. chinensis , offering valuable targets for optimizing seed propagation techniques. • Biochemical and transcriptomic analysis of dormancy and cold stratification-induced release in Cercis chinensis seeds. • Identified three modules: hormone signaling, DNA/protein synthesis, and carbon metabolism. • Cold stratification activates hormone signaling, driving cell growth / differentiation via DNA replication/ protein synthesis. • PFK1 downregulation shifts carbon flux to PPP, fueling biosynthesis and antioxidant defense. • These findings reveal new dormancy-release mechanisms and highlight targets for better seed treatments.