Combined Transcriptome and Metabolome Analysis of the Quality Change Mechanism of the ‘Pingguoli’ Pear with a Large-Fruited Bud Mutation

< 0.05) compared to NTF. Compared with the NTF, the content of total phenols and total flavonoids and the activity of antioxidant enzymes in the LFS fruits were significantly higher, while the contents of soluble sugar, reducing sugar, and soluble protein were significantly lower. Transcriptome analysis revealed that key metabolic pathways-including pentose and glucuronate interconversions, starch and sucrose metabolism, and cutin, suberine, and wax biosynthesis-were significantly enriched between NTF and LFS. These pathways may contain the specific differentially expressed genes (e.g., those involved in sugar metabolism and wax biosynthesis) identified as potential regulators of fruit size, appearance, and nutritional quality in the LFS. LC-MS/MS analysis identified key differentially accumulated metabolites, including L-arginine, caffeic acid, L-cysteine, pyridoxamine 5'-phosphate, adenosine-5'-phosphosulfate, neopentolactone D, chlorogenic acid, and gluconic acid, which are directly associated with the nutritional and antioxidant differences between LFS and NTF. The genes most related to metabolites in the three different developmental periods of the LFS and NTF were identified through combined analysis. These results provide insights for further research on bud mutation breeding and the quality formation mechanism of 'Pingguoli' pears.