This study investigates the impact of rootstock selection on the essential oil (EO) composition of clementine mandarin (Citrus clementina Hort. ex Tan.) var. SRA 63 cultivated in southern Greece. EOs were extracted from the peel and leaves of trees grafted on four commonly used rootstocks: Cleopatra mandarin, sour orange, Troyer citrange, and Swingle citrumelo. The GC-MS analysis revealed significant qualitative and quantitative differences in EO profiles across the different rootstock combinations. In peel EOs, limonene was the dominant compound, particularly in trees grafted onto Cleopatra mandarin and Swingle citrumelo, while Troyer citrange favored a more diverse chemical profile rich in oxygenated monoterpenes, sesquiterpenes, and aldehydes. Leaf EOs were characterized by high levels of sabinene, linalool, and limonene, with Swingle citrumelo promoting sabinene production and Troyer citrange enhancing limonene content and sesquiterpene diversity. Sour orange showed an intermediate effect, increasing both compound diversity and abundance. These results underscore the critical role played by rootstock in modulating the biosynthesis of volatile compounds, likely through physiological and molecular interactions with the scion. These findings offer valuable insights into optimizing EO yield and quality in citriculture and support the broader goal of valorizing Citrus by-products through targeted agricultural practices. This research contributes to the implementation of targeted agricultural practices (rootstock choice) for the development of high-value Citrus-based products with specific quality traits.

In the present study, the essential oils (EOs) of peels and leaves from the new limonime lime, ‘Eugene’ hybrid, were analyzed for the first time and compared with those of its parental plants, Citrus latifolia var. latifolia (Persian lime) and Citrus × limon cv. Zambetakis (lemon). This hybrid represents the first successful cross between these two species, exhibiting distinctive features such as aroma and shape. GC-MS analysis identified a total of 30 and 44 metabolites in the hybrid’s peel and leaf EOs, respectively. Limonene was the predominant volatile in both peels and leaves across all genotypes. In the peel EOs, the monoterpenes γ-terpinene, β-pinene, and geranial were among the most abundant compounds. In contrast, the leaf EOs showed differences between genotypes: the hybrid and Persian lime had similar volatile profiles dominated by geranial, neral, and neryl acetate, while β-pinene was only detected in lemon. Additionally, the total phenolic content and DPPH radical scavenging activity of the methanolic extracts of peels and leaves were evaluated, and revealed that lemon extracts were richer in phenolic compounds and with higher antioxidant activity compared to those of hybrid and Persian lime. Overall, the development of improved Greek varieties like the ‘Eugene’ hybrid holds significant potential to enrich the genetic diversity of Greek Citrus germplasm and broaden the commercial portfolio of citrus fruits with unique and desirable traits.