Comparative transcriptome and metabolome analyses identified key genes for carotenoid metabolic variation in Petunia and Calibrachoa

Carotenoids are widely distributed pigments that confer yellow and orange hues in flowers and fruits. Petunia hybrida and Calibrachoa hybrida, two closely related ornamental species, display distinct yellow flower pigmentation patterns. We developed a new Petunia inbred line '1408' (Pet-Yel) with vibrant yellow corollas, although they remained lighter than those of the deep-yellow Calibrachoa hybrid line '821H3' (Cal-Yel). In this study, we investigated the molecular and metabolic basis underlying yellow corolla coloration between them. By pair comparison of carotenoid metabolites between white and yellow corollas in each species, the formation of yellow corollas was primarily due to a significant increase in the levels of phytoene, β-carotene and violaxanthin. Esterified xanthophylls were notably enriched in Cal-Yel, suggesting enhanced xanthophyll esterification and improved pigment stability. To explore the underlying genetic mechanisms, we performed de novo transcriptome sequencing of Cal-Yel and conducted comparative analyses with published Petunia genome assemblies. Cal-Yel exhibited fewer gene copies in the carotenoid biosynthesis pathway but showed higher expression of key genes including PSY1-1, BCH1, and XES1, consistent with its elevated carotenoid accumulation. Notably, BCH1 and BCH2 exhibited completely opposite expression patterns between the two yellow varieties, and ChBCH1 was identified as a potential key regulator. Functional validation via transgenic overexpression of ChBCH1 in Petunia resulted in a significant increase in zeaxanthin and β-cryptoxanthin content and enhanced yellow pigmentation. These results suggest that distinct transcriptional regulatory networks and enzymatic activities underlie the yellow pigmentation in Petunia and Calibrachoa. Our findings provide new insights into carotenoid metabolism and offer genetic resources for the molecular breeding of yellow-flowered ornamental plants.