Recent Advances in DNA Methylation and Their Potential Breeding Applications in Plants

Traditional plant breeding encompasses repetitive crossing and selection based on morphological traits, while phenotypic selection has been complemented by molecular methods in recent decades. Genome editing with techniques like the CRISPR-Cas9 system is still a novel approach that is being used to make direct modifications to nucleotide sequences of crops. In addition to these genetic alterations, an improved understanding of epigenetic variations such as DNA methylation on the phenotype of plants has led to increased opportunities to accelerate crop improvement. DNA methylation is the most widely studied epigenetic mark in plants and other eukaryotes. These epigenetic marks are highly conserved and involved in altering the activities and functions of developmental signals by catalyzing changes in the chromatin structure through methylation and demethylation. Cytosine methylation (5mC) is the most prevalent modification found in DNA. However, recent identification of N6-methyladenosine (6mA) in plants starts to reveal their critical role in plant development. Epigenetic modifications are actively involved in creating the phenotype by controlling essential biological mechanisms. Epigenetic modifications could be heritable and metastable causing variation in epigenetic status between or within species. However, both genetic and heritable epigenetic variation has the potential to drive natural variation. Hence, epigenome editing might help overcome some of the shortcomings of genome editing (such as gene knockout), which can have significant off-target effects and only enables the loss of a gene’s function. In this review, we have discussed the mechanism underlying DNA methylation and demethylation in plants. Methyltransferases and demethylases are involved in catalyzing specific types of modification. We also discuss the potential role of DNA modifications in crop improvement for meeting the requirements of sustainable and green agriculture.