Developmental regulation of proanthocyanidin biosynthesis in oil palm fruit revealed by integrated omics analyses

• A dual metabolomic–transcriptomic strategy mapped proanthocyanidin pathways in oil palm. • Proanthocyanidins dominated the pigment profile and drove fruit color divergence. • Core flavonoid genes formed a conserved regulatory hub controlling PA accumulation. • F3′5′H-family genes acted as genotype-specific switches in PA biosynthesis. • The study establishes the first systems-level network for PA regulation in oil palm fruit. Proanthocyanidins are major flavonoid-derived metabolites that contribute to fruit coloration and nutritional quality in oil palm ( Elaeis guineensis Jacq.). However, the regulatory mechanisms in the exocarp remain unclear. This study integrated LC–MS/MS metabolomics and RNA-Seq transcriptomics to profile proanthocyanidin dynamics in green-fruited (AS) and black-fruited (AT) varieties at 95, 125, and 185 days after pollination. Seven proanthocyanidin-related compounds were identified, with proanthocyanidin derivatives predominating (44.5%–86.4% of total anthocyanins). Integrated correlation analysis revealed that CHS 2, CHS 1, DFR,ANS,UFGT ,and F3H were consistently positively correlated with proanthocyanidin accumulation in both varieties. Notably, F3′5′H and F3′5′H-1 exhibited completely opposite regulatory patterns between AS and AT These results reveal the regulatory network of proanthocyanidin biosynthesis in the oil palm exocarp and provide key candidate genes for fruit color improvement.