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Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection

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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.

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All data generated or analysed during this study are included in this published article (and its supplementary information files).

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Acknowledgements

This study was financially supported by the National Natural Science Foundation of China (31901859, 31901858) and the Syngenta-NEAU union foundation.

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  1. Xue Han, Qianqian Shi and Ziyi He have contributed equally to this work.

Authors and Affiliations

  1. College of Agriculture, Northeast Agricultural University, Harbin, 150030, China

    Xue Han, Qianqian Shi, Qingshan Chen & Zhaoming Qi

  2. Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China

    Qianqian Shi, Ziyi He & Wenwen Song

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XH: Conceptualization, Data curation, Writing—Original draft preparation; QS: Data curation, Visualization, Investigation, Writing—Original draft preparation; ZH: Data curation, Visualization, Investigation; WS: Reviewing and Supervision; QC: Supervision; ZQ: Conceptualization, Methodology, Supervision, Writing, Reviewing and Editing.

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Han, X., Shi, Q., He, Z. et al. Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection. aBIOTECH 3, 197–211 (2022). https://doi.org/10.1007/s42994-022-00077-2

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