Multi-Omics Analysis Unravels the Biosynthesis and Regulatory Mechanisms of Floral Scent Across Various Cultivars and Developmental Stages in Phalaenopsis

<i>Phalaenopsis</i> is one of the most economically valuable genera in the Orchidaceae family. However, the common varieties of <i>Phalaenopsis</i> in the market rarely have fragrance, greatly limiting the sustainable development of the <i>Phalaenopsis</i> industry. Here, an integrated investigation was conducted on the patterns and determinants of aroma release in <i>Phalaenopsis</i>. GC-MS/MS analysis revealed that the primary volatile organic compounds (VOCs) in 10 fragrant <i>Phalaenopsis</i> cultivars are consistent. Terpenoids, alcohols, ketones, and esters collectively accounted for an average of 66.59% of the total VOCs across these 10 varieties. By performing metabolomic and transcriptomic analyses, we investigated the variation in 1532 VOCs in four different developmental stages of <i>Phalaenopsis</i> Formosa Sweet Memory. Metabolite analysis revealed that the levels of total volatiles, terpenoids, esters, and heterocyclic compounds were significantly upregulated during the flowering stages, and Linalool, β-Ocimene, and Methyl Benzoate were selected as key metabolites. While analyzing the correlation network between aroma components synthesis and differentially expressed genes, 33 key structural genes were detected and regulated by transcription factors. <i>PAXXG356500_TPS</i>, <i>PAXXG333030_4CL,</i> and <i>PAXXG061420_SAM</i> were key genes in the terpenoids and esters' biosynthetic pathway, and they were co-expressed with aroma release. In summary, this study characterized the key metabolic pathways involved in aroma formation in <i>Phalaenopsis</i> and constructed the corresponding transcriptional regulatory network. These results laid a theoretical foundation for the subsequent research on aroma of <i>Phalaenopsis</i> and genetic engineering technology breeding.