Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean

Tissue culture is a major method for plant regeneration and for production of transgenic plants. Thus far, our knowledge of the dynamic epigenomic during tissue culture is limited. In this study, we generated epigenomes from nine different stages throughout the tissue culture process and found significant genome-wide increases of DNA methylation throughout the soybean genome. This change mostly happens in CHH (H = A, T, C) context and targets transposable elements (TEs). Subsequent analyses of corresponding transcriptomes and small RNA distributions indicate that it is associated with high activity of the RNA-directed DNA methylation (RdDM) pathway. These results provide important insights into the function of a dynamic epigenome throughout tissue culture and extends our understanding of epigenome-wide reprogramming of the DNA methylome in plants. Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance