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Updated: Aug 23, 2025
Author Spotlight: Soybean Hairy Root Transformation for the Analysis of Gene Function
Published on: May 5, 2023
Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection
Xue Han1, Qianqian Shi1,2, Ziyi He2
1College of Agriculture, Northeast Agricultural University, Harbin, 150030 China.
Abstract:
N6-methyladenosine (m6A) is a reversible epigenetic modification of mRNA and other RNAs that plays a significant role in regulating gene expression and biological processes. However, m6A abundance, dynamics, and transcriptional regulatory mechanisms remain unexplored in the context of soybean resistance to Meloidogyne incognita. In this study, we performed a comparative analysis of transcriptome-wide m6A and metabolome profiles of soybean root tissues with and without M. incognita infection. Global m6A hypermethylation was widely induced in response to M. incognita infection and was enriched around the 3' end of coding sequences and in 3' UTR regions. There were 2069 significantly modified m6A sites, 594 differentially expressed genes, and 103 differentially accumulated metabolites between infected and uninfected roots, including coumestrol, psoralidin, and 2-hydroxyethylphosphonate. Among 101 m6A-modified DEGs, 34 genes were hypomethylated and upregulated, and 39 genes were hypermethylated and downregulated, indicating a highly negative correlation between m6A methylation and gene transcript abundance. A number of these m6A-modified DEGs, including WRKY70, ERF60, POD47 and LRR receptor-like serine/threonine-protein kinases, were involved in plant defense responses. Our study provides new insights into the critical role of m6A modification in early soybean responses to M. incognita.
Supplementary Information:
The online version contains supplementary material available at 10.1007/s42994-022-00077-2.
Insights
N6-methyladenosine (m6A) RNA modification plays a key role in soybean defense against the root-knot nematode Meloidogyne incognita. This study reveals m6A hypermethylation is induced by infection, impacting gene expression and plant defense pathways.
Area of Science:
- Plant Biology
- Epigenetics
- Molecular Biology
Background:
- N6-methyladenosine (m6A) is a crucial RNA modification regulating gene expression.
- The role of m6A in soybean resistance to Meloidogyne incognita remains largely unknown.
- Understanding m6A dynamics is vital for developing resistant soybean varieties.
Purpose of the Study:
- To investigate the m6A epitranscriptomic and metabolomic profiles in soybean roots upon M. incognita infection.
- To identify m6A-modified genes and metabolites involved in the plant's defense response.
- To elucidate the regulatory mechanisms of m6A in soybean-nematode interactions.
Main Methods:
- Comparative transcriptome-wide m6A and metabolome profiling of infected and uninfected soybean roots.
- Analysis of m6A site distribution and correlation with gene expression.
- Identification of differentially expressed genes (DEGs) and differentially accumulated metabolites.
Main Results:
- Global m6A hypermethylation was induced by M. incognita infection, primarily in 3' UTRs and near coding sequences.
- 2069 m6A sites, 594 DEGs, and 103 differentially accumulated metabolites were identified.
- A negative correlation between m6A methylation and gene transcript abundance was observed.
- Key defense-related genes, including WRKY70 and ERF60, were found to be m6A-modified.
Conclusions:
- m6A modification is a critical regulator of early soybean responses to M. incognita.
- m6A-mediated gene regulation significantly influences plant defense mechanisms.
- This study provides novel insights into the epitranscriptomic landscape of soybean-nematode interactions.
