Fig. 3

ZmROS1ab regulates gene expression in endosperm. a ZmROS1ab-sensitive genes are more likely to show differential expression in endosperm. b Most of the ZmROS1ab-sensitive DEGs show downregulation. ***, P < 0.001. c The tissue expression pattern of the ZmROS1ab-sensitive DEGs. The expression data was from Yi et al. [33]. Refer to Additional file 1: Fig. S1c for details of the tissues. d ZmROS1ab-sensitive genes with preferential expression in endosperm are more likely to show differential expression. The x-axis shows the degree of endosperm preferential expression from low (small values) to high (big values), and the y-axis shows the percentage of DEGs between WT and zmros1ab mutant. e ZmROS1ab-sensitive DEGs with preferential expression in endosperm are more likely to show downregulation. The x-axis is the same as d, and the y-axis is the percentage of downregulated genes in zmros1ab mutant compared to WT. f DNA methylation profile of ZmROS1ab-sensitive DEGs across various tissues and zmros1ab mutant. g An example to show DNA methylation levels in all three contexts and the expression level of a gene that is specifically expressed in endosperm. The position of the DMRs is indicated with dashed vertical lines. h Heatmap showing the expression levels of all expressed genes and endosperm-specific genes in WT and zmros1ab mutant. i The distribution of the fold change between WT and zmros1ab. The genes are ordered based on their fold change between WT and zmros1ab