SlBES1-mediated brassinosteroid signaling suppresses flavonoid biosynthesis in tomato fruit.

With rising living standards, consumers' demand for color diversity and nutritional quality in tomato products has increased. Flavonoids are a key determinant of peel color and nutritional value in tomato fruit, where their biosynthesis is controlled by various phytohormones, including brassinosteroids (BRs). However, the underlying mechanism by which BR regulates flavonoid biosynthesis remains unclear. Here, we show that exogenous BRs suppress flavonoid accumulation, whereas reduced endogenous BR levels in RNAi lines of SlCYP90B3, a rate-limiting BR biosynthetic gene, result in increased flavonoid content in the fruit peel. We further demonstrate that BRI1-EMS-suppressor1 (SlBES1), a basic helix-loop-helix transcription factor essential for BR signaling, not only regulates fruit firmness but also represses flavonoid accumulation by directly binding to the promoters of the flavonoid biosynthetic genes SlCHS1, SlCHS2, and SlF3'H. Additionally, SlBES1 modulates a hierarchical transcriptional cascade by repressing the expression of SlMYB12, further suppressing flavonoid biosynthesis. Moreover, the homologous transcription factor brassinazole-resistant1 (SlBZR1) enhances SlBES1-mediated repression of flavonoid accumulation. Specifically, SlBES1 predominantly inhibits flavonoid biosynthesis, whereas SlBZR1 primarily enhances carotenoid pathway activity. Notably, variation in SlBES1 is correlated with flavonoid content during tomato domestication. Collectively, these results highlight a novel role for SlBES1 as a negative regulator of flavonoid biosynthesis, offering potential strategies for flavonoid biofortification in tomato.