Integrated widely targeted UPLC-MS/MS metabolomics and transcriptomics reveal MYB-linked variation in bioactive phenolics across five kiwifruit varieties

Kiwifruit ( Actinidia spp.) is valued for its bioactive phytochemicals, yet the phenolic metabolites across species and varieties remain underexplored. Using widely targeted ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) metabolomics, we profiled phenolics in five varieties representing Actinidia chinensis (‘SunGold’, ‘Guichang’, wild) and Actinidia arguta (‘Danyang flat’ DY, ‘Maolvfeng’). A total of 190 phenolic metabolites were identified. The DY strongly accumulated lignans and coumarins, with cleomiscosin C (log₂FC 14.09 vs. ‘SunGold’), fraxin, schizandriside, etc., markedly up-regulated and exhibited the highest radical-scavenging capacity. Multivariate analyses confirmed distinct varietal clustering and identified Variable Importance in Projection (VIP) > 1.0 compounds driving separation. Species-specific MYB transcription factor expression correlated with these phenolic profiles, indicating a genetic-regulatory basis for the divergent accumulation. Pathway analysis revealed that genetic background diverts carbon into specific phenolic pathways: A. arguta preferentially produces lignans/coumarins, whereas ‘SunGold’ enriches flavonoids. These results provide a metabolic and transcriptional map to support targeted breeding for nutritionally enhanced kiwifruit varieties.