Genotype and Tissue-Specific Differences of DNA Methylation in Soybean

DNA methylation is an epigenetic mark that can affect chromatin structure and gene expression without altering the DNA sequence per se. In plant, DNA methylation is generally found at both symmetrical (CG and CHG, where H is A, C, and T) and asymmetrical (CHH) sequence contexts. With the advance of sequencing technologies, genetic variations between individuals of different genetic backgrounds as well as gene expression patterns among various tissues have been extensively studied in many crop species, including soybean. However, still very little is known about variations in DNA methylation among different genotypes and tissues. In this study, we compared genome-wide methylation profiles among the 41 soybean nested association mapping (NAM) parents and three tissues (leaf, root hair and stripped root) of ‘Williams 82’. Thousands of differentially methylated regions (DMRs) were identified between genotypes as well as between tissues. The methylation differences in all three contexts (C-DMRs) were mostly associated with transposable elements (TEs), while the differences in only CG context (CG-DMRs) were found exclusively within gene bodies. Interestingly, heterochromatic blocks in pericentromeric regions of chromosome 6 (700kbp) and 9 (400kbp) showed large differences of CHG methylation without any changes in CG or CHH methylation (CHG-DMRs). Moreover, the differences in only CHH methylation (CHH-DMRs) were found mostly inside TEs, suggesting different siRNA targeting of TEs via RNA-directed DNA methylation (RdDM).