Targeted metabolomics- and transcriptomics-based investigation of carotenoid pigmentation in Phalaenopsis-Type Dendrobium hybrids

• 48 carotenoids were identified in Den-Phals, with lutein and β -carotene as the main components. • β -carotene was a key pigment for yellow Den-Phals. • LCYE acted as a key enzyme gene regulating the ratio of lutein and β -carotene. • Den-Phals holds potential role as the resource for medicinal use. Phalaenopsis -type Dendrobium hybrids (Den-Phals) stands out as globally popular tropical orchids. Carotenoids are crucial colored phytochemicals in flowers. The coloration mechanism of carotenoid s in Den-Phals flowers were investigated through targeted metabolome and transcriptome analyses. In total, 48 carotenoids were detected from 11 Den-Phals. The composition and content of carotenoids varied among these cultivars and in the different parts of the same flowers. Lutein, which improves human visual performance, had the largest content in all the samples, with an average of 52.46%, and the highest value reached 79.45%. The top 10 carotenoids, including lutein, β -carotene, neoxanthin, iolaxanthin, (E/Z)-phytoene, zeaxanthin, antheraxanthin, α -cryptoxanthin, β -cryptoxanthin, and α -carotene, collectively constituted 90% of the total carotenoids content. Among them, β -carotene, rather than lutein, was correlated with the yellow hue of floral color and was considered a key pigment. Furthermore, transcriptome sequencing of two cultivars with significant difference in carotenoid contents inferred the carotenoid metabolic pathway in Den-Phals . Seven differentially expressed genes (DEGs) were isolated: phytoene synthase ( PSY ), carotenoid isomerase ( CrtISO ), ζ-carotene isomerase ( Z-ISO ), lycopene ε-cyclase ( LCYE ), β -carotene hydroxylase ( BCH ), zeaxanthin epoxidase ( ZEP ), and 9- cis -epoxycarotenoid dioxygenase ( NCED ). Among these, LCYE was deemed a crucial enzyme gene, as it appears to govern lutein or β -carotene accumulating, thereby influencing yellow coloration of Den-Phals. The results offer valuable understanding of the carotenoid metabolic pathway and provide new guidance for breeding Den-Phals cultivars having both ornamental and medicinal traits.