Harnessing epigenetic variability for crop improvement: current status and future prospects

The epigenetic mechanisms play critical roles in a vast diversity of biological processes of plants, including development and response to environmental challenges. Particularly, DNA methylation is a stable epigenetic signature that supplements the genetics-based view of complex life phenomena. In crop breeding, the decrease in genetic diversity due to artificial selection of conventional breeding methods has been a long-standing concern. Therefore, the epigenetic diversity has been proposed as a new resource for future crop breeding, which will be hereinafter referred to as epibreeding. The induction of methylome changes has been performed in plants by several methods including chemical drugs treatment and tissue culture. Target-specific epigenetic engineering has been also attempted by exogenous RNAi mediated by virus-induced gene silencing and grafting. Importantly, the new and innovative techniques including the CRISPR–Cas9 system have recently been adopted in epigenetic engineering of plant genomes, facilitating the efforts for epibreeding. In this review, we introduce several examples of natural and induced epigenetic changes impacting on agronomic traits and discuss the methods for generating epigenomic diversity and site-specific epigenetic engineering.