Integrated volatilomic and transcriptomic analysis revealed the dynamic formation of floral scent in Hemerocallis fulva ‘Shaman’

Floral scent research in Hemerocallis remains limited despite its ornamental and edible value. In this study, the aromatic cultivar Hemerocallis fulva ‘Shaman’ was used to investigate the volatile organic compounds (VOCs) in petals across the initial, full, and final flowering stages. Metabolomic profiling combined with transcriptomic analysis via RNA sequencing was further performed to elucidate the dynamic changes in scent constituents and their underlying genetic regulation. A total of 131 VOCs were identified, with terpenoids, alcohols, and esters representing the dominant chemical classes. Twelve key aroma-active compounds, including phenethyl alcohol, linalool, ( E )-β-ocimene, farnesene, nerolidyl acetate, α-pinene, nerol, irione, (2-nitroethyl)benzene, 3-furanmethanol, nonanal, and methyl palmitate, were further identified, defining a volatile profile characterized by floral, fruity, and fresh fatty notes. Transcriptomic analysis revealed 15,189 differentially expressed genes, which were significantly enriched in metabolic pathways related to terpenoids, phenylpropanoids, and fatty acid derivatives. Within these pathways, key structural gene modules were identified, including DXS / FPPS / TPS for terpenoids, PAL / 4CL / CAD for phenylpropanoids, and LOX / ADH / AAT for fatty acid derivatives, each showing strong temporal correlation with the accumulation of their corresponding volatiles. Additionally, from 2,547 predicted transcription factors (TFs), 58 candidate regulators closely associated with the 12 key volatiles were identified, with bHLH (9), MYB (7), AP2/ERF (6), NAC (5), and WRKY (4) families prominently represented. This study systematically uncovered the dynamic variation of floral scent components and identified key structural gene modules and candidate TFs associated with their biosynthesis, providing a foundation for understanding aroma formation in Hemerocallis and supporting future molecular breeding of fragrant cultivars. • Terpenoids and phenylpropanoids dominated the floral scent at full bloom. • Floral scent transitioned to fatty-acid derivatives during senescence. • DXS-FPPS-TPS and PAL-CAD gene modules correlated with stage-specific volatiles. • bHLH, MYB, NAC, and WRKY transcription factors coordinated scent biosynthesis. • Integrated metabolite-gene-TF framework assisted aromatic Hemerocallis breeding.