Multi-Omics Reveals Protected Cultivation Improves Chinese Plum (Prunus salicina L.) Quality via Light-Regulated Sugar Metabolism

The Chinese plum (<i>Prunus salicina</i> L.), 'Zuili', is a geographically protected cultivar that is valued for its high polyphenol levels and distinctive flavor. Light availability strongly influences sugar accumulation and secondary metabolism in plum fruit, yet the molecular processes associated with quality variation under protected cultivation remain unclear. Here, we compare three cultivation systems-multi-span greenhouse (M), retractable electric rain shelter (R), and conventional open field (CK)-to evaluate their effect on fruit quality using integrated transcriptomic and metabolomic analyses. Field trials showed that M treatment increased fruit sweetness by 28.10% versus CK (14.68 vs. 11.46 °Brix, <i>p</i> < 0.001) without yield loss and significantly improved vertical fruit diameter. RNA-seq analysis identified 7561 and 7962 upregulated genes in the M and R treatments compared to CK, respectively, with significant functional enrichment in pathways related to sucrose metabolism, light-response, and ethylene-mediated signaling. Untargeted metabolomic signaling identified 1373 metabolites, with shading treatments increasing the abundance of several sugar-conjugated compounds (e.g., epicatechin 3-O-(2-trans-cinnamoyl)-β-D-allopyranoside). Multi-omics integration revealed coordinated changes in gene expression and metabolite abundance, suggesting that controlled light environments are associated with the concurrent modulation of sugar metabolism and phenylpropanoid-related pathways. These patterns were supported by the upregulation of GT2-family glycosyltransferase genes and the accumulation of lignin-related flavonoid precursors, such as pinobanksin and pinobanksinol. Collectively, these results highlight statistically robust associations between light-regulated cultivation practices and fruit quality traits, providing a molecular framework for optimizing protected cultivation strategies to enhance both the sensory and nutritional attributes of <i>P. salicina</i> fruit without compromising yield.