Nymphaea ‘Eldorado’, a valuable water lily, is a well-known fragrant plant in China. Studying the temporal and spatial characteristics of the floral components of this plant can provide a reference for the further development and utilization of water lily germplasm resources. In this study, headspace solid-phase microextraction (HS-SPME) combined with gas chromatography–mass spectrometry (GC-MS) was used to explore the types and relative contents of floral components at different flowering stages (S1: bud stage; S2: initial-flowering stage; S3: full-flowering stage; S4: end-flowering stage) and in different floral organs of N. ‘Elidorado’, combined with the observation of the microscopic structure of petals. A total of 60 volatile organic compounds (VOCs) were detected at different flowering stages, and there were significant differences in floral VOCs at different flowering stages and in different flower organs. The volatile compounds of N. ‘Eldorado’ can be divided into seven chemical classes,, namely, alkenes, alcohols, esters, aldehydes, ketones, alkanes, and others; the most common were alkenes and alkanes. A total of 39, 44, 47, and 42 volatile compounds were detected at S1, S2, S3, and S4. The VOCs present in high concentrations include benzaldehyde, benzyl alcohol, benzyl acetate, trans-α-bergamotene, α-curcumene, cis-α-farnesene, and so on. The types and total contents of volatiles at the full-flowering stage were higher than at other flowering stages. Comparing the VOCs in different parts of flower organs, it was found that the contents of alcohols, esters, and aldehydes were greatest in the petals, the alkenes in stamens were abundant with a relative content of up to 54.93%, and alkanes in the pistil were higher than in other parts. The types and total contents of volatiles in the stamens of N. ‘Eldorado’ were higher than those in other flower organs; they were the main part releasing fragrance. The observation of petal microstructure revealed that the size and quantity of the papillae on the epidermises of petals, the number of intracellular plastids, and the aggregates of floral components (osmophilic matrix granules) were significantly higher at the full-flowering stage than at the other flowering stages. This study suggested the main flowering stage and location at which the floral VOCs are released by N. ‘Eldorado’ and provided a reference for guiding the breeding of this water lily, exploring genetic patterns and developing related products.

Fragrance lotus (Nymphaea hybrid) is a tropical interspecific cultivar characterized by large flowers and high scent intensity, offering dual potential for ornamental commerce and natural fragrance extraction. Floral scent determines both economic value and pollinator attraction, yet the biosynthetic organs and metabolic routes remain undocumented. To fill this gap, single flowers of the high-aroma cultivar ‘Eldorado’ at full anthesis were dissected into petal (PE), stamen (ST) and pistil (PI); each organ was subjected to untargeted LC-MS/MS metabolomics and Illumina RNA-seq. Organ-specific gene–metabolite co-expression networks were constructed by pairwise integration of transcript and metabolite matrices. All three organs formed distinct clusters in principal-component space. Compared with PE, 6221, 3352 and 5891 differentially expressed genes (DEGs) together with 30, 24 and 39 differentially accumulated metabolites (DAMs) were identified in ST, PI and PE, respectively. The phenylpropanoid biosynthesis pathway (map00940) was the only route simultaneously enriched at both transcript and metabolite levels; 59 DEGs mapped to this pathway co-linearly with three scent-related DAMs. ST contained the highest concentration of scent-active volatiles; phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate-CoA ligase (4CL) and benzaldehyde reductase (BAR) were all significantly up-regulated in this organ, driving the accumulation of p-coumaric acid that is subsequently channeled into benzyl alcohol via side-chain cleavage and BAR-mediated reduction, thereby generating the characteristic fragrance of Nymphaea. This study provides the first organ-level resolution of scent biosynthesis and metabolic flux partitioning in fragrance lotus, furnishing molecular targets for directed aroma improvement and efficient natural fragrance extraction.