A modulatory role of CG methylation on gene expression in soybean implicates its potential utility in breeding

作者：Ying Wang, Hongwei Xun, Jiameng Lv, Weina Ju, Yuhui Jiang, Meng Wang, Ruihong Guo, Mengru Zhang, Xiaoyang Ding, Liu B, Chunming Xu · 发表于：Plant Biotechnology Journal · 年份：2025 · DOI：10.1111/pbi.14606 · 被引用次数：14 · 研究领域：Soybean genetics and cultivation、Legume Nitrogen Fixing Symbiosis、Plant Molecular Biology Research

Summary Cytosine methylation (mCG) is an important heritable epigenetic modification, yet its functions remain to be fully defined in important crops. This study investigates mCG in soybean following the loss‐of‐function mutation of two GmMET1 genes. We generated knockout mutants of GmMET1s by CRISPR‐Cas9 and conducted comprehensive methylome and transcriptome analyses. Our findings unravel the functional redundancy of the two GmMET1 s, with GmMET1b being more critically involved in maintaining mCG levels, and complete knockout of both copies is lethal. We establish that genome‐wide mCG levels scale with aggregated expression of GmMET1s . We identify a set of mCG‐regulated genes whose expression levels were quantitatively modulated by upstream, body, or downstream mCG. Moreover, we find genes that were negatively regulated by upstream or body mCG are enriched in specific biological processes such as that of jasmonic acid metabolism. Notably, >80% of the differentially methylated genes (DMGs) in the mutants also exist as DMGs in natural soybean populations. Phenotypically, mutants that are heterozygous for GmMET1a and homozygous for GmMET1b knockouts ( GmMET1a +/− GmMET1b −/− ) exhibited early flowering, which was inherited by their selfed progeny ( GmMET1a +/+ GmMET1b −/− ) with otherwise normal growth and development. Moreover, mutation of either GmMET1s , with slight reduction of mCG levels and similar phenotypes compared to the wild type under normal conditions, showed ...