Cold stratification breaks seed dormancy in an endangered medicinal plant Ferula sinkiangensis: Integrative hormonal and transcriptional insights for conservation.

Ferula sinkiangensis K. M. Shen is an endangered medicinal plant endemic to Xinjiang, China, whose deep physiological seed dormancy severely restricts population regeneration and sustainable utilization. To elucidate the mechanisms by which cold stratification promotes dormancy release, we conducted an integrative analysis combining targeted hormone metabolomics (UHPLC-MS/MS), transcriptomics (RNA-seq), and germination phenotyping across three stratification stages (0, 10, and 20 d). Germination assays confirmed that cold stratification effectively broke seed dormancy in a time-dependent manner, with optimal performance achieved at 20 d (germination rate 55% versus 0% in fresh seeds). Metabolomic profiling revealed a systemic reconfiguration of the endogenous hormonal network, characterized by a pronounced decline in abscisic acid (93% reduction by day 10) and stage-specific accumulation of gibberellin GA20 (day 20), accompanied by coordinated downregulation of stress-related hormones including jasmonic acid and auxin. Transcriptomic analysis demonstrated extensive transcriptional reprogramming initiated at the early stage, with stage-specific enrichment in plant hormone signal transduction, MAPK signaling, and late activation of cell cycle pathways. Weighted gene co-expression network analysis further identified distinct gene modules temporally correlated with hormonal dynamics, revealing a "sensing-transition-execution" regulatory architecture. Collectively, these findings establish a biphasic model of dormancy release driven by sequential ABA depletion and GA20 accumulation, and provide a multi-omics framework guiding artificial propagation protocols for this endangered species.