Integrated Metabolomic and Transcriptomic Analysis Reveals the Roles of Cutin, Suberin, and Flavonoid Metabolism in Apple Peel Deterioration Under Non-Bagging Cultivation

Non-bagging apple cultivation, which is time-saving, labor-saving, and cost-effective, represents the future direction of apple cultivation in China. However, compared with bagging cultivation, it degrades fruit appearance quality, characterized by rough peels and dull colors, with the underlying physiological and molecular mechanisms remaining unclear. This study used 'Tianhong 2' Fuji apples, grafted onto SH dwarfing rootstock, and integrated transcriptomics-metabolomics to explore these mechanisms. Results showed that non-bagging-cultivated apple peels had higher chlorophyll and carotenoid contents but lower anthocyanin content than those of bagging-cultivated ones. Transcriptome sequencing identified 1571 differentially expressed genes (DEGs: 1269 upregulated, 302 downregulated). Functional analysis revealed that the decline in fruit appearance quality was primarily associated with secondary metabolite biosynthesis, lipid metabolism, and carbohydrate metabolism, and 34 candidate genes were identified. Metabolomic analysis detected 394 differentially expressed metabolites (DEMs), 38 of which were closely related to the non-bagging-induced appearance degradation, mainly lipids, organic oxygen compounds, and organic acids and their derivatives. Integrated analysis of DEGs and DEMs indicated the involvement of multiple critical metabolic pathways, including cutin, suberin and wax biosynthesis; starch and sucrose metabolism; cyanoamino acid metabolism; and phenylpropanoid and flavonoid biosynthesis. Compared with bagging-cultivated apples, non-bagging-cultivated apples exhibited faster starch degradation and higher soluble sugar accumulation. Additionally, the accumulation of specific metabolites [e.g., quercetin (HMDB0005794, HMDB03249, LMPK12112097), and suberin components (LMFA01170020, LMFA01050437, HMDB0031885)], along with elevated organic acid levels, contributed to peel roughness and dull coloration. These findings further enrich the theoretical basis for the formation of fruit quality in Fuji apples under non-bagging cultivation and provide valuable theoretical guidance for the practical application of this cultivation mode.