Maize Genomics and Genetics 2025, Vol.16, No.6, 325-333 http://cropscipublisher.com/index.php/mgg 325 Research Insight Open Access Dynamic DNA Methylation Landscapes in Maize Roots Under Salt Stress Shanjun Zhu, Wei Wang Institute of Life Sciences, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: wei.wang@jicat.org Maize Genomics and Genetics, 2025, Vol.16, No.6 doi: 10.5376/mgg.2025.16.0030 Received: 30 Oct., 2025 Accepted: 16 Dec., 2025 Published: 31 Dec., 2025 Copyright © 2025 Zhu and Wang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhu S.J., and Wang W., 2025, Dynamic DNA methylation landscapes in maize roots under salt stress, Maize Genomics and Genetics, 16(6): 325-333 (doi: 10.5376/mgg.2025.16.0030) Abstract Salt stress is one of the main abiotic factors limiting the yield of maize (Zea mays L.), especially having a significant impact on root growth, water absorption and ion homeostasis. Recent studies have shown that epigenetic regulatory mechanisms, especially DNA methylation, play a significant role in plants’ response to adverse stress. However, there is still a lack of systematic research on the dynamic changes of the whole-genome DNA methylation map of maize roots under salt stress conditions. This study reviews the physiological and molecular response characteristics of maize root systems under salt stress, as well as the biological functions of DNA methylation in plant stress responses. It introduces the types of methylation and their detection techniques, analyzes in detail the dynamic change characteristics and functional enrichment pathways of methylation profiles under salt stress, and compares the methylation differences between typical salt-tolerant and sensitive maize varieties. It reveals the possible mechanism of epigenetic regulation in the formation of salt tolerance. This study explored the dynamic regulatory mechanism of DNA methylation in maize roots under salt stress, providing a new perspective for a deeper understanding of plant epigenetic responses and also offering a theoretical basis and data support for the development of salt-tolerant maize varieties. Keywords Maize (Zeamays); Salt stress; DNA methylation; Epigenetic regulation; Whole-genome methylation sequencing 1 Introduction Once the yield of corn is restricted, it is often related to abiotic stress, and salt stress, especially in arid or semi-arid regions, is one of the most influential factors. High-salt soil can disrupt the normal absorption of water and nutrients, disrupt the ionic balance, causing corn plants to grow shorter, have smaller leaves, and even significantly reduce the biomass above and below ground. Eventually, the yield also "shrinks" (Maimaiti et al., 2025). The most obvious impact is still on the early growth stage of corn. During this period, it is particularly sensitive to salt, the roots are prone to deformation, photosynthesis is also likely to have problems, and the overall growth of the plant is not good. Whether the plant can withstand these pressures largely depends on whether it can maintain its own metabolism and physiological balance. Therefore, finding ways to enhance the salt tolerance of corn is clearly an urgent and valuable task (Farooq et al., 2015). Some regulatory methods, though seemingly insignificant, can be very effective in adverse circumstances. DNA methylation is one of them. In fact, it is not a recent focus. As a typical epigenetic modification, it has long been proven to stabilize the genome and regulate gene expression. Under salt stress, its "actions" are particularly frequent, especially in key pathways such as ion transport, antioxidation, and hormone signaling. Changes in methylation are often linked to the activation or deactivation of these pathways (Zhang et al., 2024). Genes closely related to root systems, such as ZmPP2C and ZmEXPB2, have been observed to show significant methylation changes in high-salt environments - some regions are demethylated while others become heavier. These changes basically directly affect their expression levels and thus drive the entire chain of stress response. In addition to these, there is another mechanism worth mentioning, which is RNA-mediated DNA methylation (RdDM). It is not new in the regulatory process, but regulatory factors like ZmKTF1 have been confirmed to be involved, which indeed makes people look at its position in maize salt tolerance in a new light (Wang et al., 2024). Of course, all of this is not that simple. The regulatory pattern is not "one-size-fits-all". Different genotypes and tissue locations may lead to completely different DNA methylation behaviors. This difference actually reflects the complexity of epigenetic regulation and once again indicates that for plants to truly adapt to salt environments, it relies on a very subtle regulatory system (Sun 2018; 2022).
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