Integrated metabolomics and transcriptomics reveal the molecular basis of cultivar-specific floral scent biosynthesis in fingered citron (Citrus medica)

Finger citron ( Citrus medica L. var. sarcodactylis) is a distinctive resource possesses significant medicinal, ornamental, and industrial value. While its rich aroma is central to both economic importance and scientific research, the molecular mechanisms underlying key aromatic compound biosynthesis remain unclear. This study employed integrated metabolomic and transcriptomic analyses to systematically characterize the volatile organic compound (VOC) profiles and elucidate molecular basis of aroma formation across three fingered citrons. Gas chromatography-mass spectrometry (GC-MS) analysis identified 1476 metabolites, with terpenoids being the most abundant class (21.1%). Tissue type (flower vs. leaf) was the primary factor influencing VOC composition, while cultivar differences were more pronounced in floral tissues. Notably, relative odor activity value (ROAV) analysis identified three key VOCs that distinguish ‘Hongxiutianxiang’ from Golden fingered citron: germacrene D, β-damascone and 2-phenylethyl 3-methylbutanoate. Transcriptomic analysis revealed cultivar-specific gene expression patterns, with weighted gene co-expression network analysis (WGCNA) identifying co-expression modules strongly correlated with these key metabolites and constructed a co‑expression gene network associated. Through integrated phylogenetic analysis, differential expression profiling, molecular docking validation, we identified Cm205460 as a putative germacrene D synthase, Cm012490 as a candidate carotenoid cleavage dioxygenase for β-damascone synthesis, and by vitro enzyme assay identified Cm129590 as key BAHD acyltransferases responsible for 2-phenylethyl 3-methylbutanoate production. These findings provide comprehensive insights into the metabolic and genetic basis of aroma diversity in fingered citrons, establishing a foundation for molecular breeding and quality improvement of aromatic citrus cultivars.