Muhammad Junaid Rao, Kangjian Song, Sijiu He, Shirong He, Yuanqiao Li, Ima Mulyama Zainuddin, Yubo Chen, Xinnian Du, Wei Liu, Munsif Ali Shad, Maryam Tahira, X Duan, Bingsong Zheng, Liuyuan Bao, Shunqiang Yang, Mingzheng Duan
Phenolic compounds are vital bioactive constituents in fruits, yet modern strawberry breeding has often reduced their diversity. Here, we employed a multi-omics approach integrating UPLC-MS/MS-based metabolomics and RNA-seq transcriptomics to investigate the divergence in phenolic profiles and their transcriptional regulation between a wild strawberry (Fragaria nilgerrensis, HM) and three cultivated varieties (white ‘Danxue’ (DX), pink ‘Fenyu’ (FY), and red ‘Red Face 99’ (RF)). The wild HM genotype exhibited higher antioxidant activity and a significantly more complex phenolic profile, dominated by high-abundance galloylated and benzoylated glucosides (e.g., digallic acid methyl ester, salicylic acid-2-O-glucoside) that were largely absent or depleted in cultivated fruits. In contrast, the cultivated varieties displayed specialized yet simplified profiles: DX accumulated hydroxycinnamoyl galactonic acids, FY was enriched in feruloylated glucosides, and RF was characterized by coumaroyl-glucose derivatives. Transcriptomic analysis identified a set of MYB transcription factors (e.g., FxaYL_531g0581170, FxaYL_642g0175720) significantly upregulated in wild HM, with strong correlations to key bioactive phenolics such as 4-hydroxybenzoate and salicylic acid derivatives. These findings illustrate how selective breeding has reshaped phenolic composition through alterations in MYB regulatory networks. The wild strawberry germplasm thus represents a valuable natural reservoir for biofortification strategies aimed at restoring the nutritional and functional quality of modern strawberry cultivars.