Metabolomic and Transcriptomic Analysis Reveals Flavonoid Biosynthesis in Color-Associated Culivars and AmbHLH360 Modulating Anthocyanin Accumulation in Antirrhinum majus

Plant coloration is a key ornamental trait of Antirrhinum majus that is mainly governed by flavonoid biosynthesis. We conducted integrated metabolomic and transcriptomic analyses on four differently colored cultivars (white: BAI, yellow: H, pink: F, purple: ZY) of the Potomac cut flower series. Cultivar-specific dominant flavonoids were detected, and H exhibited the highest total flavonoid (4.75 g/kg) and carotenoid (0.071 mg/g) contents. Metabolomic profiling identified 327 flavonoid metabolites (13 subgroups), with flavones (28.44%) and flavanols (25.69%) as the most abundant. Transcriptomic analysis identified 7716 differentially expressed genes (DEGs) enriched in phenylpropanoid, flavonoid, and carotenoid biosynthesis pathways. Twenty-four key structural genes related to flavonoid/anthocyanin biosynthesis were screened, with expression patterns correlated with metabolite accumulation. Eight DEG transcription factor families were identified, and AmbHLH360 was a candidate regulator of flavonoid biosynthesis. Heterologous overexpression of AmbHLH360 in tobacco increased petal redness, anthocyanin (up to 3.0-fold), and flavonoid (up to 1.1-fold) contents, and upregulated downstream biosynthetic genes. These findings clarify the metabolic basis of A. majus flower color variation and provide candidate genes for horticultural molecular breeding.