Integrative Multi-Omics Reveals Tissue-Specific Postharvest Changes in Blueberry Fruit

Postharvest cold storage is essential for maintaining blueberry fruit quality, yet the molecular basis of tissue-specific responses during storage remains poorly understood. Here, we integrated widely targeted metabolomics and transcriptomics to characterize peel and pulp responses during 6 weeks of storage at 4 °C. Metabolomic profiles revealed pronounced tissue specialization, with peel enriched in flavonoids, terpenoids, and phenylpropanoid-derived metabolites, whereas pulp accumulated amino acids and other primary metabolites. In contrast, transcriptomic variation was dominated by storage, indicating a largely conserved response across tissues. Multi-omics analyses using DIABLO, MOFA2, and network analysis identified 65 genes and 58 metabolites associated with storage-related and tissue-specific variation. These analyses highlighted jasmonate- and oxylipin-associated pathways, antioxidant responses, membrane lipid remodeling, and phenylpropanoid metabolism, alongside reduced expression of aquaporins and cell wall-modifying genes. Overall, these findings provide a systems-level view of blueberry storage responses and identify candidate molecular processes associated with postharvest quality and storage performance.