Physiological, transcriptomic and metabolomic analyses reveal pericarp color divergence in longan

Longan ( Dimocarpus longan Lour.) is an important subtropical fruit, and pericarp color is a key quality trait affecting its commercial value. Systematic investigations into the mechanisms governing red/white pericarp formation in longan remain lack. This study analyzed phenotypic, metabolic, transcriptomic, and hormonal profiles of red (HLY) and white (BLY) pericarp longan at maturity. HLY had higher anthocyanin content and a* values, while BLY showed higher L* and b* values. Targeted LC-MS/MS identified 51 anthocyanins, and HLY enriched in cyanidin/delphinidin derivatives, while BLY in procyanidins. Transcriptomics identified 29 anthocyanin structural genes with distinct expression between HLY and BLY. Thirty of 40 detected hormones were differentially accumulated. DlFLS was highly expressed in HLY, and its transient overexpression in strawberries enhanced red pigmentation and anthocyanin content, and protein three-dimensional structure prediction together with yeast one-hybrid assays demonstrated that DlMYB12 is capable of binding to the DlFLS promoter. Results indicate longan pericarp color variation is governed by differential anthocyanin accumulation, structural gene regulation, hormonal signaling, and DlFLS -mediated anthocyanin promotion, aiding quality genetic improvement.