Jin Wang , Lin Liu , Congbiao You

Tropical Microbial Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China
Author    Correspondence author
Legume Genomics and Genetics, 2025, Vol. 16, No. 5   
Received: 08 Aug., 2025    Accepted: 20 Sep., 2025    Published: 09 Oct., 2025

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.

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.

Epigenetics; Nodule development; Legume-rhizobia symbiosis; DNA methylation; Chromatin remodeling