Fig. 5

Associations between DMRs and gene expression. a The genomic distribution of genes and their associated DMRs. The x-axis indicates the genomic positions of DMRs, while the y-axis is the genomic positions of corresponding genes. The color reflects the direction of association between gene expression and DMRs, with blue for positive associations and orange for negative associations. Note there are more orange dots (negative associations) in the plots of CG and CHG methylation, and more blue dots (positive associations) in the plot of CHH methylation. b The distance between the DMR and the gene transcription start site (TSS) is evaluated for DMR-gene expression associations. The x-axis is the log₁₀ (downstream) or − log₁₀ (upstream) value of the distance from DMR to the TSS, while the y-axis is the number of associations. The color indicates the direction of associations with darker shades representing lower P value. c Summary plot for the proportion of negative associations for DMRs with varying distance to gene TSS. Note the closer the DMR to gene, the more negative associations for CG and CHG methylation and the more positive associations for CHH methylation. d Comparison between leaf and kernel expression data using associations within 1 Mb from DMR to TSS. e The expression levels of genes in leaf (kernel) which only show significant associations in kernel (leaf) tissue. The left plot shows P value of significant gene-DMR associations, and the right plot shows levels of gene expression. Gray color means that the data are not available because of low/no expression of the gene in that tissue. f The proportion of DMRs associated with gene expression that also have a significant association with SNPs