Epigenetic modification for horticultural plant improvement comes of age

Abstract Our era has witnessed tremendous technique advances and mechanically epigenetic improvement in plant epigenetics, mainly including histone post-translational modifications (PTMs) and DNA methylation, which have been characterized as playing vital roles in development processes and plant response to environmental factors. Recently, chemical modifications on RNAs like 5-methylcytosine (m5C) and N6-methyladenosine (m6A) have been revealed as a new layer of epigenetic marks to regulate gene translation efficiency in model plant Arabidopsis thaliana and with later discovery of horticultural species like tomato (Solanum lycopersicum) and poplar (Populus trichocarpa). In model plants, these epigenetic modifications on DNA, RNA, and histone tails largely trigger innumerable studies on how epigenetic mechanisms are involved in gene regulation and biological functions. As an emerging research field in horticultural plants, epigenetic modifications have bloomed in fruit development and ripening, grafting, and bud dormancy. In this Review, we have demonstrated recent advances of high-throughput sequencing methods, summarized epigenetic enzymatic systems to install, remove and recognize epigenetic marks, discussed essential roles of epigenetic regulation, and proposed how innovative computation techniques like machine learning and deep learning are set to understanding epigenetic regulation mechanisms in horticultural plants. We also raise future perspectives on how epigenetic modifications act as new additions for understanding their roles in gene expression that is required for development and environmental adaptation in horticultural plants.