Integrating transcriptomics with metabolomics reveals the differential mechanisms underlying the color and volatile substances of Amomum tsao-ko

Amomum tsao-ko is a significant medicinal and edible plant, recognized for its distinctive aroma. The pericarp color varies among different cultivars, yet the relationship between pericarp color and both edible and medicinal values, as well as the mechanisms regulating color variation, remains poorly understood. To elucidate the molecular mechanisms underlying variations in pericarp color and the active ingredients in different parts of the fruits, we investigated the transcriptome and metabolome of the pericarp, placenta, and seeds in A. tsao-ko cultivars with dark red, red, and brown pericarps. Compared to the cultivar with a brown pericarp, the majority of anthocyanin-related genes were found to be up-regulated in the dark red A. tsao-ko pericarp, potentially inducing the accumulation of pelargonidine-3-O-rutinoside, pelargonidine-3-O-glucoside, cyanidin-3-O-rutinoside, cyanidin-3-O-glucoside and cyanidin-3-O-arabinoside in the dark red pericarp. Seeds of dark red A. tsao-ko are predominantly composed of diterpenoids, with the expression of geranylgeranyl diphosphate synthase (GGPPS) being up-regulated. In contrast, brown A. tsao-ko is abundant in monoterpenoids, with most genes in the methylerythritol phosphate pathway (MEP) exhibiting up-regulation. β -Pinene is most abundant in the pericarp, while citral is rich in the seeds and placenta. This study establishes a comprehensive database for the metabolite and transcript profiles in different fruit parts and cultivars. These data can be applied to the selection and breeding of A. tsao-ko varieties, the differential utilization of various fruit parts, and the screening of genes involved in the synthesis of active ingredients. • Anthocyanins are more abundant in dark red Amomum tsao-ko . • The biosynthesis genes of anthocyanins are significantly up-regulated in dark red A. tsao-ko . • Terpenoids constitute the primary volatile compounds in A. tsao-ko . • Most genes in the MEP pathway are upregulated in the red strain.