Conclusion

This study provides a comprehensive, multi‐organ and multi‐cultivar metabolomic characterization of Prunus avium , highlighting the interplay between genotype, organ specificity, and environmental variability in shaping phenylpropanoid metabolism.

By integrating untargeted and quantitative metabolomic analyses of leaves and fruits collected across different orchards and growing seasons, our results indicate that cultivar‐associated variation represents a major component of specialized metabolite accumulation in both organs, within the environmental range considered here. At the same time, a pronounced organ‐specific specialization of phenylpropanoid metabolism was observed. Fruit and leaf metabolomes displayed largely independent cultivar‐dependent accumulation patterns, suggesting that genotype‐related regulation of secondary metabolism operates in an organ‐specific manner. This finding is consistent with the distinct physiological functions of vegetative and reproductive tissues, in which similar classes of metabolites may fulfill different roles or have different biological significance.

Notably, despite this overall independence, a subset of low‐abundance metabolites exhibited conserved cultivar‐dependent accumulation patterns in both leaves and fruits. These compounds may reflect shared regulatory mechanisms and potentially similar functional relevance across organs, pointing to a coordinated component of phenylpropanoid metabolism that transcends tissue specialization.

Collectively, these findings expand current knowledge of specialized metabolism in sweet cherry by showing that, within each organ, phenolic profiles contain a reproducible genotype‐associated component that remains detectable across different growing seasons and orchard locations. By incorporating leaf metabolomics alongside fruit profiling, this work underscores the importance of multi‐organ approaches for elucidating genotype‐dependent metabolic variation and provides a valuable framework for future studies on phenylpropanoid function, plant adaptation, and the valorisation of sweet cherry genetic resources.