Metabolomics and transcriptomics uncover spatial regulation of flavonoids in Belamcanda chinensis (L.) Redouté rhizome endodermis

This study preliminarily explored the molecular regulation mechanism of flavonoid differences between the inner and outer parts of the endodermis of the Belamcanda chinensis (L.) Redouté rhizome. Untargeted metabolomics was used for metabolomics analysis to screen differential metabolites of flavonoids. Transcriptome analysis was performed using high-throughput transcriptome sequencing (RNA-seq) to screen for differentially expressed enzyme genes and transcription factors. Transcriptome and metabolome association analyses were used to screen for key enzyme genes. Metabolomic analysis identified 10 differential metabolites associated with flavonoid biosynthesis pathways, including catechin, luteolin, hesperetin and so on. Transcriptomic analysis revealed 22 differentially expressed genes related to flavonoid biosynthesis pathways, including 2 CHS, 2 PAL, and 9 POD genes. Through integrative analysis, we hypothesized that 22 genes, specifically BcCHS1, BcCHS2, BcHCT1, BcHCT2, BcPAL1, and BcANS, are key enzymes responsible for the differential accumulation of flavonoid components. Most flavonoid metabolites were highly expressed in the outer part of the endodermis compared to the inner part. Key enzyme genes, including BcCHS1, BcCHS2, BcHCT1, BcHCT2, BcPAL1, BcANS, likely play crucial roles in the spatial accumulation differences of flavonoid in and out of the endodermis of B. chinensis rhizome. This study preliminarily analyzed the molecular regulation mechanism of flavonoid differential accumulation, laying a foundation for quality improvement and molecular breeding of B. chinensis.