Integrated analysis of metabolome and transcriptome reveals the special flavor substances in pomelo fruits

• Significant differences between the two varieties of pomelo. • DEGs and DAMs were significantly enriched in phenylpropanoid biosynthetic pathway. • Liangping pomelo up-regulated the genes involved in furanocoumarin accumulation. • The reduction of numbness in pomelo may be related to a number of factors. • Sugar content in pomelo increased with longer storage time. Liangping Pomelo (LP) is one of the three most famous pomelo varieties in China and is favored by consumers for its sweet and refreshing aroma and numbing aftertaste. However, the substances responsible for its numbing flavor remain unknown. In this study, LP (with numbing flavor) and Humi Pomelo (HM, without numbing flavor) were adopted as research materials to investigate the potential material basis and molecular mechanism of numbing flavor. Combined transcriptomic and metabolomic analyses revealed that differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were significantly enriched in the phenylpropanoid biosynthetic pathway, suggesting a potential link between this pathway and the numbing substances in LP. Metabolomic analysis further indicated that Eugenol, Cinnamaldehyde, and Furanocoumarins, potential numbing compounds in the phenylpropanoid biosynthesis pathway, were present at higher levels in LP than in HM. Transcriptome analysis identified 11 key genes involved in the synthesis of potential numbing flavor substances. These findings could provide a scientific foundation for future research on the numbing flavor components in LP and offer valuable insights into the selection and breeding of new varieties and the biosynthesis of phenylpropanoid compounds.