Persimmon anthracnose, a severe disease caused by the hemibiotrophic fungus Colletotrichum horii, poses a substantial threat to China’s persimmon industry. Previous research showed that ‘Kangbing Jianshi’ cultivar exhibits strong resistance to anthracnose. Notably, ‘Kangbing Jianshi’ branches exhibit greater lignification compared with the susceptible ‘Fuping Jianshi’ cultivar. In this study, higher lignin content was observed in ‘Kangbing Jianshi’ compared with ‘Fuping Jianshi’, and this difference was associated with disease resistance. Transcriptome and metabolome analyses revealed that the majority of differentially expressed genes and differentially accumulated metabolites were primarily enriched in the phenylpropanoid biosynthesis and lignin synthesis pathways. Furthermore, significant upregulation of DkCAD1, a pivotal gene involved in lignin metabolism, was observed in the resistant cultivar when inoculated with C. horii. Transient overexpression of DkCAD1 substantially increased lignin content and improved resistance to C. horii in a susceptible cultivar. Furthermore, through yeast one-hybrid (Y1H) assays, we identified two WRKY transcription factors, DkWRKY8 and DkWRKY10, which interacts with the DkCAD1 promoter and induces its activity. Overexpression of DkWRKY8 and DkWRKY10 not only increased leaf lignin content but also enhanced persimmon tolerance to C. horii. Moreover, the expression levels of DkCAD1, DkWRKY8, and DkWRKY10 were significantly increased in response to salicylic acid and jasmonic acid in the resistant cultivar. These findings enhance our understanding of the molecular functions of DkWRKY8, DkWRKY10, and DkCAD1 in persimmons, as well as their involvement in molecular breeding processes in persimmons.

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.

Epigenetic modifications alter the gene activity and function by causing change in the chromosomal architecture through DNA methylation/demethylation, or histone modifications without causing any change in DNA sequence. In plants, DNA cytosine methylation (5mC) is vital for various pathways such as, gene regulation, transposon suppression, DNA repair, replication, transcription, and recombination. Thanks to recent advances in high throughput sequencing (HTS) technologies for epigenomic “Big Data” generation, accumulated studies have revealed the occurrence of another novel DNA methylation mark, N6-methyladenosine (6mA), which is highly present on gene bodies mainly activates gene expression in model plants such as eudicot Arabidopsis (Arabidopsis thaliana) and monocot rice (Oryza sativa). However, in non-model crops, the occurrence and importance of 6mA remains largely less known, with only limited reports in few species, such as Rosaceae (wild strawberry), and soybean (Glycine max). Given the aforementioned vital roles of 6mA in plants, hereinafter, we summarize the latest advances of DNA 6mA modification, and investigate the historical, known and vital functions of 6mA in plants. We also consider advanced artificial-intelligence biotechnologies that improve extraction and prediction of 6mA concepts. In this Review, we discuss the potential challenges that may hinder exploitation of 6mA, and give future goals of 6mA from model plants to non-model crops.