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

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.