Integrative metabolomic, transcriptomic and sensory profiling of daodi Huangsi-Yujin (Radix Curcuma longa): Unveiling quality distinctions for a marker-guided processing strategy

Sichuan Province is the daodi source of Huangsi-Yujin (HSYJ, Radix Curcuma longa ). Despite their similar appearances, traditional and improved HSYJ cultivars coexist, complicating quality standardization. This study explored the significant phenotypic diversity between these cultivars, primarily in aroma and color, and established a marker-guided quality retention strategy. Non-targeted GC×GC-TOFMS volatilomics revealed that even within the same daodi region, improved cultivars exhibited higher germacrone but lower turmerone content than traditional ones. Transcriptomic analysis confirmed that this chemical divergence is driven by genetic factors. Furthermore, HS-SPME-GC/Orbitrap-MS integrated with electronic nose assessments identified variety-specific aromatic signatures. Quantitative LC-MS analysis correlated the superior curcuminoid levels in traditional HSYJ with their intense yellow hue (elevated CIE L*a*b* values). To bridge the gap between chemical identification and industrial application, these identified volatile markers and curcuminoids guided a tailored, sequential processing strategy. Supercritical CO 2 extraction was first utilized to capture the authentic aroma fraction, followed by the recovery and stabilization of curcuminoids via microencapsulation. This integrated framework not only elucidates the genetic and chemical basis of HSYJ quality but also demonstrates how marker-guided processing ensures the consistent, modernized production of high-quality daodi herbal products. • Multi-omics reveal genetic and chemical variations between HSYJ cultivars. • GC×GC-TOFMS differentiates cultivars and medicinal parts of daodi HSYJ. • HS-SPME-Orbitrap-MS and E-nose decode variety-specific aroma signatures. • Curcuminoid levels correlate with intense yellow hue via colorimetry. • Marker-guided processing validates the industrial applicability of HSYJ markers.