Engineering DNA Methylation Dynamics in Plants: Strategies from Detection to Deployment

DNA methylation, a conserved epigenetic modification, influences several crucial functions, including gene expression, silencing of transposable elements, genomic stability, and growth and development. While advances in whole-genome bisulfite sequencing enable the identification of numerous DNA methylation sites in plants, their utility depends on characterizing DNA methylation marks for specific traits and applying them effectively in crop improvement. Central to both goals is the ability to investigate and manipulate DNA methylation at specific loci. This review focuses on recent breakthroughs in site-specific DNA methylation and demethylation in plants. Methods for detecting DNA methylation in crop plants, highlighting their respective advantages and limitations are also evaluated. We further examine the recruitment of different DNA-binding proteins to target regions. By synthesizing current research on site-specific DNA methylation and demethylation in plants, this review offers guidance on selecting the most effective strategies for site-specific DNA methylation editing. These advances hold considerable potential for crop breeding by unlocking phenotypic variation from the same genetic material, without altering the underlying DNA sequence, a transformative approach for agricultural improvement.