LC-MS/MS reveals variation in bioactive flavonoid profiles and MYB regulatory networks in wild vs. cultivated strawberries (white, pink, red)

Strawberries ( Fragaria × ananassa ) are prized for bioactive flavonoids and anthocyanins, contributing to antioxidant capacity and health benefits. However, decades of breeding for yield and shelf-life have eroded their phytochemical diversity. To explore this trade-off, we compared wild strawberries ( Fragaria nilgerrensis , HM) with three cultivated varieties (pink-FY, red-RF, white-DX) using integrated LC-MS/MS metabolomics and transcriptomics. Wild HM strawberries contained twice the vitamin C (134.2 mg/100g), 2.5 × more total flavonoids (138.7 mg/100g), and higher antioxidant activity (367 μg Trolox/g) than commercial varieties. In contrast, red-fruited RF showed abundant anthocyanins (pelargonidin-3-glucoside 6.6 % abundance), while the wild HM genotype accumulated higher levels of flavonoids, with neohesperidin, lonicerin, hyperin and ternatumoside II collectively representing 20.9 % of total flavonoids - concentrations 3–169 times greater than those observed in the three commercial varieties (FY, RF, DX). Transcriptomic analysis (RNA-seq, Illumina HiSeq 2500) revealed distinct MYB transcription factor associations: FxaYL_611g0111200 (MYB66) showed strong positive correlation with anthocyanin biosynthesis in RF (r = 0.92, ∗∗p < 0.005 ), while FxaYL_242g0472670 (MYB44-like) was significantly associated with HM's unique antioxidant flavonoid profile (r = 0.96, ∗∗∗p < 0.0001 ). These regulatory relationships were corroborated by hierarchical clustering demonstrating varietal-specific expression patterns and principal component analysis (82.6 % variance explained), collectively providing molecular targets for enhancing nutritional quality in strawberry breeding programs. • Tetraploid strawberry (HM) exhibit 2.5 × higher flavonoids than octoploid cultivars (FY/RF/DX). • Anthocyanin-rich RF contrasts with HM's flavonoid diversity, revealing trade-offs between pigmentation and stress adaptation. • Candidate MYB genes (e.g., MYB66 , MYB44-like ) correlate with metabolic shifts ( p < 0.005), but functional validation is required. • Wild germplasm offers potential for nutrient-dense breeding, though future studies should investigate environmental interactions. • Findings guide functional food development, with caveats on flavonoid stability across diverse growing environments.