Introduction

Prunus avium L. is an arboreal fruit species comprising hundreds of varieties and is of considerable commercial and nutritional importance worldwide (Blando and Oomah 2019; Yang et al. 2025). Sweet cherry fruits are valued not only for the organoleptic qualities but also for the high content of phenolic compounds, which contribute to antioxidant capacity and human health benefits (Kelley et al. 2018; Blando and Oomah 2019; Gonçalves et al. 2019). Fruits are a rich source of bioactive phenolic compounds, including flavonoids, hydroxycinnamic acids, and anthocyanins, which have been widely studied for their antioxidant, anti‐inflammatory, cardioprotective, and neuroprotective properties (Blando and Oomah 2019; Antognoni et al. 2020; Manach et al. 2004; Rana et al. 2022; El‐Saadony et al. 2024; Gonçalves et al. 2024). Clinical and epidemiological studies have shown that cherry consumption may reduce oxidative stress, improve vascular function, and alleviate inflammation‐related conditions such as arthritis and gout (Zhang et al. 2012; Arbizu et al. 2023; Colletti et al. 2025). The growing scientific interest in the health‐promoting properties of sweet cherries has consequently driven numerous efforts to characterize their phytochemical profiles and to understand the factors that influence metabolite accumulation (Commisso et al. 2017; Clodoveo et al. 2023; Mineață et al. 2024; Ceccarelli et al. 2022; Nie et al. 2023).

Among these factors, both genetic and environmental components have been shown to modulate the metabolic composition of sweet cherry fruits, with the genotype emerging as the predominant determinant of both qualitative and quantitative metabolite variation (Commisso et al. 2017; Martini et al. 2017; Boskov et al. 2022). Studies have demonstrated that cultivar identity significantly affects the levels of certain phenolic compounds, including anthocyanins and flavonols, often representing a major source of variation together with growing conditions such as orchard location or climate and the type of rootstock (Commisso et al. 2017; Martini et al. 2017; Boskov et al. 2022).

While much of the current metabolomics research has understandably focused on the fruit, given their economic value and relevance to human health, other tissues such as leaves remain comparatively underexplored, despite their recognized role in the biosynthesis and accumulation of specialized metabolites. In various woody and herbaceous species, leaves have been shown to accumulate substantial levels of phenolic compounds potentially involved in stress response and defense (Andreotti et al. 2006; Kumar et al. 2023; Liu et al. 2024; Jiao et al. 2024; Wang et al. 2025). In sweet cherry, only a limited number of studies have investigated the metabolite composition of leaves, and these have been largely driven by economic considerations, focusing on the recovery of bioactive compounds from leaves regarded as by‐products, while their biological and ecological significance has received comparatively little attention (Dziadek et al. 2019; Nunes et al. 2021). These studies indicate that foliar tissues may contain even higher concentrations of phenolic compounds than fruits, particularly hydroxycinnamic acid derivatives and flavonols.

However, systematic investigations of the sweet cherry leaf metabolome across cultivars and growing seasons remain scarce, and the extent to which leaf and fruit metabolic profiles are coordinated or follow distinct, organ‐specific trajectories remains poorly understood. Moreover, leaves are commonly regarded as metabolically plastic organs, as their physiology and metabolism are strongly influenced by external factors, such as light, temperature, and biotic interactions. Consequently, whether stable, genotype‐associated organization of specialized metabolic pathways can be detected in leaf tissues remains an open question.

In this study, we combined untargeted metabolomic profiling with absolute quantification of major phenylpropanoids to compare leaves and fruits of sweet cherry cultivars at full fruit maturity. Our objective was (i) to investigate tissue‐specific metabolic channels within the phenylpropanoid pathway and (ii) to determine whether phenylpropanoid pathway organization in leaves exhibits a reproducible genotype‐associated structure across different orchards and growing seasons, analogous to that previously observed in fruits, thereby extending the analysis of genotype‐associated metabolic organization to a vegetative tissue traditionally regarded as highly plastic.