Additional file 1: Table S1. Primers used in gene cloning and vector construction. Table S2. Primers used for amiRNA plasmid construction. Table S3. HPLC–MS running parameters. Table S4. Primers used for RT-qPCR analysis of gene expression. Fig. S1. Image of isolated maize protoplasts. Fig. S2. The HPLC chromatogram and the MS profiles of all the benzoxazinoids. Fig. S3. Benzoxazinoid levels in W22 and bx2::Ds transposon knockout mutants. Fig. S4. ZmBX1 transcript level in maize protoplasts

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... r overexpressing target gene. Fig. S5. The contents of HDMBOA-Glc, MBOA, M2BOA, and DIM2BOA-Glc in protoplasts transfected with ZmBX1 over time. Fig. S6. ZmBX1 transcript level in maize protoplasts after silencing with gene-specific amiRNA. Fig. S7. ZmMYB61 transcript level in maize protoplasts after overexpressing target gene. Fig. S8. The changes of benzoxazinoid contents induced by overexpressing ZmMYB61. Fig. S9. Transcription levels of target genes after overexpression or silencing. Fig. S10. Schematic representation of the predicted bHLH protein binding motifs (E-boxes) in the promoters of benzoxazinoid biosynthesis genes.