Figure 1

Cluster analysis of 77 genes with seed-specific CHH DMRs based on gene expression at stages S2, S6, and S8. Gene clusters based on gene transcription patterns in cotyledon at three stages and DNA methylation in DMRs in ^mCHH, ^mCHG and ^mCG contexts. The green to red color gradient represents low to high gene expression, respectively. Genes with 1) more than 30% DNA methylation changes among three different seed stages S2, S6, and S8, 2). statistically significant changes in gene expression and 3). a negative correlation (PCC < −0.85) between gene expression and methylation level were used for cluster analysis.