Non-CG DNA hypomethylation promotes photosynthesis and nitrogen fixation in soybean

Non-CG DNA methylation, a plant-specific epigenetic mark mainly regulated by chromomethylase (CMT), is known to play important roles in <i>Arabidopsis thaliana</i>. However, whether and to what extent non-CG DNA methylation modulates agronomic traits in crops remain to be explored. Here, we describe the consequences of non-CG DNA hypomethylation on development, seed composition, and yield in soybean (<i>Glycine max</i>). We created a <i>Gmcmt</i> mutant line lacking function of all four <i>CMT</i> genes. This line exhibited substantial hypomethylation of non-CG (CHG and CHH) sites. Non-CG hypomethylation enhanced chromatin accessibility and promoted or repressed the expression of hundreds of functionally relevant genes, including upregulation of <i>GOLDEN-LIKE 10</i> (<i>GmGLK10</i>), which led to enhanced photosynthesis and, unexpectedly, improved nitrogen fixation efficiency. The <i>Gmcmt</i> line produced larger seeds with increased protein content. This study provides insights into the mechanisms of non-CG methylation-based epigenetic regulation of soybean development and suggests viable epigenetic strategies for improving soybean yield and nutritional value.