GmMYB4 Positively Regulates Isoflavone Biosynthesis via the GmMAPK6 ‐ GmMYB4 ‐ MBW Module in Soybean

ABSTRACT Isoflavones, a class of bioactive compounds predominantly found in leguminous plants, are largely responsible for their beneficial effects on human health. Although MYB transcription factors (TFs) are known to be crucial regulators of isoflavone biosynthesis in soybean, the precise mechanisms underlying their regulatory functions remain poorly understood. Here, we identified GmMYB4 as a key positive regulator of isoflavone accumulation through a genome‐wide association study and functional characterisation. GmMYB4 interacts with bHLH TFs within the MYB‐bHLH‐WD repeat protein (MBW) complex, modulating the assembly of the complex and regulating the expression of downstream targets, including GmIFS2 and GmANS3 , which are involved in the biosynthesis of isoflavone and anthocyanin, respectively. These two pathways compete for common precursors, representing competitive metabolic branches. Furthermore, GmMAPK6 promotes isoflavone accumulation by positively regulating the expression of GmMYB4 and genes in the isoflavone biosynthesis pathway. Importantly, GmMAPK6 phosphorylates the 39th serine residue of GmMYB4. These findings reveal a GmMAPK6‐GmMYB4‐MBW regulatory module as a critical mechanism for the fine‐tuning of isoflavone biosynthesis, offering novel insights and potential strategies for the development of high‐quality soybean varieties.