Abstract

Background: Peach fruit quality can be compromised by cold storage, a postharvest practice required for long-distance export that can trigger chilling injury and metabolic disturbances affecting sugars, organic acids, and other metabolites. Preharvest practices such as thinning modify source-sink relationships and fruit development, potentially influencing susceptibility to chilling stress. Objectives: This study aimed to determine whether commercial thinning alters fruit susceptibility to cold storage damage and to identify metabolic processes associated with chilling tolerance in two nectarine varieties with contrasting sensitivity, 'Magique' (tolerant) and 'Red Pearl' (sensitive). Methods: Fruits from thinned (TH) and unthinned (UTH) trees were subjected to cold storage (0 degrees C, 21 days) followed by ripening, and evaluated for physiological parameters, sugar and organic acid composition by HPLC, and phenylpropanoid-related metabolites by 1H-NMR. A genome-scale metabolic model was built to model fruit metabolism using COBRApy. Results: Thinning increased fruit size in both varieties. Magique exhibited overall metabolic stability across thinning treatments and cold storage. Red Pearl, in contrast, showed broad metabolic fluctuation in response to external stimuli. Integration of transcriptomic data and metabolic modeling identified quinate-centered reactions as candidate regulatory nodes associated with phenylpropanoid flux during ripening and post-chilling recovery. Conclusions: These findings indicate that modulating quinate metabolism during early ripening may help improve chilling tolerance and highlight the phenylpropanoid pathway as a central metabolic axis modulated by both pre- and postharvest practices, with implications for fruit quality management.