Integrated Metabolomic and Transcriptomic Analysis Reveals Bioactive Compound Diversity in Organs of Saffron Flower

Abstract Saffron stigma, derived from Crocus sativus L., has long been revered in global traditional medicine and continues to hold significant market value. However, despite the extensive focus on saffron stigma, the therapeutic potential of other floral components remains underexplored, primarily due to limited insights into their complex molecular architectures and chemical diversity. To address this gap, we performed a comprehensive metabolomic analysis of various floral organs utilizing advanced analytical platforms, including GC–MS and UPLC‐MS/MS. This in‐depth profiling revealed a diverse array of 248 metabolites, encompassing amino acids, sugar derivatives, fatty acids, flavonoids, vitamins, polyamines, organic acids, and a broad spectrum of secondary metabolites. Distinct correlation patterns among these metabolites were identified through PCA and PLS‐DA, highlighting unique metabolomic signatures inherent to each floral organ. We further integrated these metabolomic findings with our transcriptomic data, enabling a detailed understanding of the molecular and metabolic variations across different floral organs. The pronounced abundance of differentially expressed genes and metabolites in the stamen (424), leaf (345), tepal (196), stigma (177), and corm (133) underscores the intricate regulatory networks governing source‐to‐sink partitioning and dynamic metabolic processes. Notably, our study identified several bioactive compounds, including crocin, picrocrocin, crocetin, safranal, cannabielsoin, quercetin, prenylnaringenin, isorhamnetin, pelargonidin, kaempferol, and gallic acid, all of which exhibit potential therapeutic properties. In conclusion, this comprehensive analysis significantly enhances our understanding of the molecular mechanisms driving the biosynthesis of apocarotenoids, cannabinoids, anthocyanins, and flavonoids in saffron, thereby providing valuable insights and paving the way for future research in this area.