Metabolomics Connecting Genomes and Phenomes in Plant Molecular Breeding—A Special Focus on Mediterranean Agronomical Important Tree Species

The interest in Mediterranean species has grown exponentially in recent decades, driven by their distinctive organoleptic properties and the high content of bioactive compounds beneficial to human health. This study presents a comprehensive review of current knowledge on the alterations in metabolomicMetabolomics profiles associated with the biosynthesis of functional metabolitesFunctional metabolites in response to abiotic stressors, namely salinity, extreme temperatures, drought and UV exposure, in five agronomically significant Mediterranean tree species: olive (Olea europaea L.), cork oak (Quercus suber L.), pine tree (Pinus pinaster Ait. and Pinus pinea L.), and carob tree (Ceratonia siliqua L.). Furthermore, considering that the reliability of metabolomicMetabolomics data depends on the methodologies employed for sample preparation and analysis, we provide an extensive overview of the primary methods for comprehensive metabolome extraction and the analytical techniques utilized for subsequent analysis.