DNA methylation, an evolutionarily conserved epigenetic mechanism, is crucial for controlling gene activity and ensuring genomic integrity. Altered methylation patterns can profoundly affect plant development, often resulting in atypical phenotypes. The regulation of these methylation states relies on the coordinated actions of de novo methylation, maintenance, and active demethylation, orchestrated by specialized enzymes within distinct pathways. This review delves into the diverse roles of DNA methylation in plants, offering an in-depth analysis of the enzymes and regulatory factors involved. We explore how these elements function within the broader epigenetic framework, focusing on their contributions to silencing transposable elements, modulating gene expression, and shaping chromatin architecture. The review also examines the significance of DNA methylation in plant development, particularly its role in adapting to biotic and abiotic stresses. Lastly, we highlight its potential for driving innovations in crop breeding, emphasizing its applicability in advancing sustainable agriculture.

Background: As one of three essential nutrients, potassium is regarded as a main limiting factor for growth and development in plant. Sweet potato (Ipomoea batatas L.) is one of seven major food crops grown worldwide, and is both a nutrient-rich food and a bioenergy crop. It is a typical ‘K-favoring’ crop, and the level of potassium ion (K⁺) supplementation directly influences its production. However, little is known about the transcriptional changes in sweet potato genes under low-K⁺ conditions. Here, we analyzed the transcriptomic profiles of sweet potato roots in response to K⁺ deficiency to determine the effect of low-K⁺ stress on this economically important crop. Results: The roots of sweet potato seedlings with or without K⁺ treatment were harvested and used for transcriptome analyses. The results showed 559 differently expressed genes (DEGs) in low and high K⁺ groups. Among the DEGs, 336 were upregulated and 223 were downregulated. These DEGs were involved in transcriptional regulation, calcium binding, redox-signaling, biosynthesis, transport, and metabolic process. Further analysis revealed previously unknow genes involved in low-K⁺ stress, which could be investigated further to improve low K⁺ tolerance in plants. Confirmation of RNA-sequencing results using qRT-PCR displayed a high level of consistency between the two experiments. Analysis showed that many auxin-, ethylene- and jasmonic acid-related genes respond to K⁺ deficiency, suggesting that these hormones have important roles in K⁺ nutrient signaling in sweet potato. Conclusions: According to the transcriptome data of sweet potato, various DEGs showed transcriptional changes in response to low-K⁺ stress. However, the expression level of some kinases, transporters, transcription factors (TFs), hormone-related genes, and plant defense-related genes changed significantly, suggesting that they have important roles during K⁺ deficiency. Thus, this study identifies potential genes for genetic improvement of responses to low-K⁺ stress and provides valuable insight into the molecular mechanisms regulating low K⁺ tolerance in sweet potato. Further research is required to clarify the function of these DEGs under low-K⁺ stress.

Background: Wheat (Triticum aestivum L.) is a major cereal crop that is grown worldwide, and it is highly dependent on sufficient N supply. The molecular mechanisms associated with nitrate uptake and assimilation are still poorly understood in wheat. In plants, NRT2 family proteins play a crucial role in NO₃^– acquisition and translocation under nitrate limited conditions. However, the biological functions of these genes in wheat are still unclear, especially their roles in NO₃^– uptake and assimilation. Results: In this study, a comprehensive analysis of wheat TaNRT2 genes was conducted using bioinformatics and molecular biology methods, and 49 TaNRT2 genes were identified. A phylogenetic analysis clustered the TaNRT2 genes into three clades. The genes that clustered on the same phylogenetic branch had similar gene structures and nitrate assimilation functions. The identified genes were further mapped onto the 13 wheat chromosomes, and the results showed that a large duplication event had occurred on chromosome 6. To explore the TaNRT2 gene expression profiles in wheat, we performed transcriptome sequencing after low nitrate treatment for three days. Transcriptome analysis revealed the expression levels of all TaNRT2 genes in shoots and roots, and based on the expression profiles, three highly expressed genes (TaNRT2-6A.2, TaNRT2-6A.6, and TaNRT2-6B.4) were selected for qPCR analysis in two different wheat cultivars (‘Mianmai367’ and ‘Nanmai660’) under nitrate-limited and normal conditions. All three genes were upregulated under nitrate-limited conditions and highly expressed in the high nitrogen use efficiency (NUE) wheat ‘Mianmai367’ under low nitrate conditions. Conclusion: We systematically identified 49 NRT2 genes in wheat and analysed the transcript levels of all TaNRT2s under nitrate deficient conditions and over the whole growth period. The results suggest that these genes play important roles in nitrate absorption, distribution, and accumulation. This study provides valuable information and key candidate genes for further studies on the function of TaNRT2s in wheat.

DNA methylation, a highly conserved epigenetic modification, plays an essential role in regulating gene expression and maintaining genome stability. Aberrations in DNA methylation patterns can significantly disrupt plant developmental processes, often leading to abnormal phenotypes. These methylation states are governed by a dynamic interplay of de novo methylation, maintenance methylation, and active demethylation, mediated by a suite of specialized enzymes operating under distinct regulatory pathways. This review explores the multifaceted roles of DNA methylation in plants. We provide a comprehensive overview of methylases, demethylases, and regulatory factors, elucidating how these components interact within the broader methylation machinery. Key functions of DNA methylation, including its roles in transposon silencing, gene expression regulation, and chromatin interactions, are systematically examined. Additionally, the impact of DNA methylation on plant development is analyzed, with a focus on its involvement in responses to biotic and abiotic stressors. Finally, we discuss the potential applications of DNA methylation in crop improvement, highlighting its promise for advancing modern agricultural practices.

DNA methylation is a conserved and vital epigenetic modification that plays essential roles in plant growth, development, and responses to environmental stress. Cytosine-5 DNA methyltransferases (C5-MTases) and DNA demethylases (dMTases) are key regulators of DNA methylation dynamics. However, a comprehensive characterization of these gene families in sweet potato has remained elusive. In this study, we systematically identified and analyzed eight C5-MTase and five dMTase genes in the genomes of diploid (Ipomoea trifida, 2n = 2x = 30) and autohexaploid (Ipomoea batatas, 2n = 6x = 90) sweet potato. Phylogenetic, structural, and synteny analyses revealed a high degree of conservation among these genes, suggesting their essential roles during evolution. Promoter analysis uncovered multiple cis-acting elements, particularly those responsive to light and hormones. In addition, we examined the expression profiling of IbC5-MTases and IbdMTases genes during storage root development, revealing that several were highly expressed during the early and rapid expansion stages. These findings suggest that C5-MTases and dMTases may contribute to the regulation of storage root formation in sweet potato through epigenetic mechanisms, offering valuable insights for future functional studies and epigenetic breeding efforts.

Background: Potassium is one of the three essential nutrients and is regarded as a main limited factor for growth and development in plant. Sweet potato (Ipomoea batatas L.) is one of the seven major food crops grown worldwide, and it is both a nutrient-rich food and a bioenergy crop. Sweet potato is a typical “K-favoring” crop, and the level of potassium ion (K⁺) supplementation directly influences its production. However, little is known about the transcriptional changes in sweet potato genes under low-K⁺ condition. To uncover the effect of low-K⁺ stress, we analyzed the transcriptomic profiles of sweet potato roots in response to K⁺ deficiency.Result: The roots of sweet potato seedlings with or without K⁺ treatment were harvested and used for transcriptome analyses. The results showed 559 differently expressed genes (DEGs) in low and high K⁺ groups. Among the DEGs, 336 were upregulated and 223 downregulated. These DEGs were involved in transcriptional regulation, calcium binding, redox-signaling, biosynthesis, transport, and metabolic process. In the result, some new genes were founded that involved in low-K⁺ stress, which can be further investigated to improve low K⁺ tolerance in plant. Confirmation of RNA-seq results using qRT-PCR displayed a high level of consistency between the two experiments. Our analysis showed that many auxin-related genes, ethylene-related genes and jasmonic acid-related genes responsed to K⁺ deficiency, indicated that these hormones may play more important roles in K⁺ nutrient signaling in sweetpotato. Conclusions: According to the transcriptome data, fewer sweetpotato genes showed transcriptional changes in response to low-K⁺ stress. However, the expression level of some kinases, transporters, transcription factors, hormone-related genes, and plant defense related genes were markedly changed, suggesting that they play important roles during K⁺ deficiency. This study identifes potential genes for genetic improvement of low-K⁺ stress and provides valuable insight into the molecular mechanisms regulating low K⁺ tolerance in sweet potato. Further research is required to clarify the founction of these significant changed genes under low-K⁺ stress.