Legume Genomics and Genetics 2025, Vol.16, No.5, 225-233 http://cropscipublisher.com/index.php/lgg 225 Review and Progress Open Access Role of Epigenetic Modifications in Regulating Nodule Development Jin Wang, Lin Liu, Congbiao You Tropical Microbial Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: congbiao.you@hitar.org Legume Genomics and Genetics, 2025 Vol.16, No.5 doi: 10.5376/lgg.2025.16.0023 Received: 08 Aug., 2025 Accepted: 20 Sep., 2025 Published: 09 Oct., 2025 Copyright © 2025 Wang et al., 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: Wang J., Liu L., and You C.B., 2025, Role of egenetic mdifications in rgulating ndule dvelopment, Legume Genomics and Genetics, 16(5): 225-233 (doi: 10.5376/lgg.2025.16.0023) Abstract Nodulation in legumes is a highly regulated symbiotic process crucial for biological nitrogen fixation, which is crucial for sustainable agriculture. This study investigates how epigenetic modifications-specifically DNA methylation, histone modifications, and small RNAs-coordinate gene expression programs during distinct stages of nodule development. We first investigated the epigenetic landscape of legume root cells, highlighting the dynamic changes in methylation and the histone code during nodule formation. We then delved into the role of epigenetic mechanisms in early symbiotic signaling events, such as nodulation factor recognition, root hair coiling, and infection filament formation, and analyzed chromatin remodeling during cortical cell reprogramming and nodule organogenesis. We further investigated how environmental conditions such as nutrient availability and abiotic stress influence these epigenetic responses and assessed the transgenerational inheritance of nodulation traits. A detailed case study in Medicago truncatula, utilizing mutants and whole-genome analyses, elucidated the functional importance of specific epigenetic marks during nodule formation. Finally, we explore the translational potential of manipulating epigenetic regulators through genome editing and breeding to enhance the legume-rhizobium symbiosis. This study highlights the importance of integrating epigenomics with functional and systems biology to explore new strategies to improve nitrogen fixation efficiency in legumes. Keywords Epigenetics; Nodule development; Legume-rhizobia symbiosis; DNA methylation; Chromatin remodeling 1 Introduction During the symbiotic process between leguminous plants and rhizobia, there is a particular phenomenon that is often mentioned-nodulation. This is not a simple plant growth change, but a special development of root tissue that forms a structure called a "root nodule" (Wu and Yan, 2024). It is precisely these structures that provide a living space for nitrogen-fixing bacteria, enabling them to "convert" nitrogen in the air into a form that plants can absorb (Huang, 2024). Especially in environments where the soil is infertile or lacks fertilizer, this natural nitrogen fixation mechanism becomes particularly crucial. However, when it comes to the development of root nodules, it is not as simple as just the interaction between bacteria and plants. Many people may not know that the epigenetic mechanisms within plants play the role of regulatory switches in this process. The epigenetics mentioned here does not refer to gene mutations and does not involve changes in the DNA sequence itself, but it can directly affect whether genes are expressed, when they are expressed, and to what extent. For instance, operations like DNA methylation and histone modification may not show any trace on the surface, but in fact, they leave "marks" on genetic activity. And changes in non-coding RNA and chromatin structure are also involved. They interact with each other, providing flexibility for plants to "choose" which genetic program to use in different environments. Much of our past understanding of these mechanisms originated from the medical field, such as animal research or tumor systems. But in fact, in plants, these mechanisms are equally applicable and even highly conservative. Therefore, they have also received increasing attention and discussion in regulating the development of root nodules in leguminous plants (Yang et al., 2023). This study attempts to approach it from this perspective. We hope to sort out the existing research results on the relationship between epigenetic modifications and root tumor formation, and see exactly what roles these
RkJQdWJsaXNoZXIy MjQ4ODYzNA==