B-BOX22 isoforms activate expression of MYBs and elicit blue light-induced flavonoid biosynthesis in soybean.

Soybean (Glycine max) accumulates a substantial amount of flavonoids, including anthocyanins and flavonols, which play essential roles in both plant growth and human health. While blue light promotes flavonoid biosynthesis, the regulatory circuitry governing this process remains poorly characterized. Here, we demonstrate that blue light stimulates flavonol and anthocyanin accumulation in soybean hypocotyls by inducing the B-box transcription factor GmBBX22. Mechanistically, GmBBX22 transcripts are alternatively spliced under blue light, generating 3 isoforms (designated as X1, X2, and X3). Intriguingly, the truncated isoforms X2 and X3 induce flavonol and anthocyanin biosynthesis through distinct regulatory cascades. Rather than directly targeting the biosynthesis flavonol synthase gene (GmFLS) or dihydroflavonol 4-reductase gene (GmDFR), which encode key enzymes for metabolic flux partitioning between flavonols and anthocyanins, X2 and X3 specifically activate the expression of GmMYB12 and GmMYB90, respectively. Subsequent functional analyses revealed that these MYB transcription factors induce GmFLS and GmDFR expression to coordinate flavonol and anthocyanin accumulation. Collectively, our work delineates a splicing-dependent regulatory module where GmBBX22 isoforms mediate light quality adaptation in soybean through divergent transcriptional programming of flavonoid metabolism.