Biochemical mechanisms underlying the differences in fruit characteristics among three kumquat varieties

To elucidate different fruit trait mechanisms among Changshou (FOT) (Fortunella obovata Tanaka), Liuyang (FCSLY) (Fortunella crassifolia Swingle), and Huapi (FCSHP) (Fortunella crassifolia Swingle) kumquats, fruit traits, and their metabolite compositions were comprehensively analyzed. The main factors affecting fruit sweetness and bitterness are the sucrose and limonin contents. Differential metabolite analysis showed that FOT peels had the highest redness and more up-regulated anthocyanin and carotenoid compounds. Therefore, anthocyanin and carotenoid metabolites were related to the kumquat peel color. FOT peels had the highest flavonoid content. A total of 1719 metabolites were identified using non-targeted metabolomics, Flavonoid metabolites are more abundant in kumquat peels than in seeds, so the peel’s medicinal value is higher. The total limonin content in seeds is higher than in peels, so the seeds are used as raw materials for extracting limonin compounds. This study analyzed the biochemical mechanisms of fruit trait differences in three kumquat (Fortunella Swingle) varieties and provided a reference for targeted kumquat development and utilization.