Metabolic Characteristics and Flavonoid Differences in Peel and Flesh of Three Kumquat Cultivars Based on Non-Targeted Metabolomics

Untargeted metabolomics based on ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to explore metabolite differences in the peel and flesh tissues of three Rong’an kumquat cultivars. A total of 5043 metabolites were detected. Principal component analysis (PCA) revealed clear separation of metabolic profiles among different cultivars. Significantly altered metabolites were screened with thresholds of VIP > 1 and |Log2FC| ≥ 1.0. A total of 193 flavonoid metabolites were annotated, among which 84 flavones and 28 flavonols were the dominant subclasses. Flavonoid profiles exhibited significant cultivar- and tissue-specific differences. Huapi kumquat (HP) and Cuimi kumquat (CM) showed tissue-specific anthocyanin accumulation, with anthocyanins enriched mainly in peel tissues, while Youpi kumquat (YP) accumulated abundant chalcones and flavanones. The flavonoid metabolic variation in peel tissues was greater than that in flesh tissues. 2′,6′-dihydroxy-4,4′-dimethoxychalcone (with log2FC up to 8.44) and xanthohumol were identified as candidate metabolic markers. KEGG pathway enrichment analysis further revealed distinct tissue-biased metabolic features. Specifically, cultivar-related metabolic variation in peel was associated with diterpenoid and lipid metabolic pathways, whereas flesh metabolic divergence was linked to indole alkaloid biosynthesis, histidine metabolism, and folate biosynthesis. This study systematically elucidated the metabolic characteristics and flavonoid differences in the peel and flesh of three kumquat cultivars, providing candidate metabolic markers and theoretical support for the evaluation and utilization of kumquat germplasm resources.