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

Abstract

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.

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

“…This could be one of the most interesting and significant results of the present study. Methylation data have been employed in plant breeding to investigate and improve flowering time, disease susceptibility and abiotic stress response (Mercé et al 2020 ; Shaikh et al 2022 ), and have enabled genomic diversity expansion and discovery of cis-regulatory elements (Xu et al 2019 ; Crisp et al 2020 ). The present study highlights the spectrum of methylation patterns and putative epialleles in oilseed rape with special implications on seed formation.…”

The recent possible strategies for breeding ultraviolet-B-resistant crops

“…Finding people or populations with innate UVB tolerance can be aided by evaluating the natural variation in DNA methylation patterns among various plant genotypes. Breeders can choose potential candidates for additional breeding attempts by screening against particular DNA methylation patterns linked to UVB resistance [ 15 , 16 ]. Additionally, recent developments in genome editing techniques, like CRISPR-based systems, have the capacity to change DNA methylation patterns in a precise way.…”

“…UVB radiation can also alter how certain genes' DNA is methylated. These gene-specific variations in DNA methylation may be related to DNA repair, UVB stress response, and other biological UVB tolerance-related processes [ [15] , [16] , [17] ].…”

Emerging Role of Folate-Mediated One Carbon Metabolism in Leukemia: A Review

“…It is also a crucial biochemical mechanism for life transmission. Cell division and the regulation of gene expression through imprinting and epigenesis are both fueled by the methylation of DNA and histones (Shaikh et al 2022). Methylation, a basic epigenetic mark important for controlling the expression of genes, is typically linked to gene suppression.…”