Genotype-Associated Phytochemical Variability and Multi-Omics Integration in Olea europaea L. and Citrus bergamia: Perspectives on Precision Development of Mediterranean Nutraceuticals

Background: The Mediterranean Diet (MedDiet) is a global benchmark for the prevention of cardiometabolic diseases and healthy aging, with Olea europaea L. (O. europaea L.) and Citrus bergamia Risso et Poiteau (bergamot) serving as primary sources of bioactive molecules such as phenols, in particular flavonoids. Recent evidence highlights a paradigm shift from traditional agricultural yield toward a precision-nutrition model, in which the health-promoting potential of these species is increasingly recognized to arise from the interplay between genetic background and environmental factors. Objectives This review summarised current evidence on how genetic variability drives the metabolic fingerprints of olive and bergamot, exploring the integration of genomic, transcriptomic, and metabolomic data to identify cultivars with superior nutraceutical value. Results: Evidence suggests that phytochemical profiles of O. europaea L. and Citrus species, including bergamot, are shaped by the interaction between genetic background and environmental conditions, with genotype contributing significantly to metabolic variability. Specific O. europaea L. and Citrus genotypes display distinct metabolic fingerprints characterized by different bioactive compound profiles, potentially underlying variations in antioxidant, cardioprotective, lipid-lowering, and anti-inflammatory properties. Conclusions: The integration of high-resolution genotyping and metabolic profiling supports the selection of superior genotypes for standardized, evidence-based nutraceuticals. Future advances in precision breeding are expected to further enhance the health-promoting traits of these Mediterranean species.