Comprehensive analysis of m6A-regulatory genes in soybean uncovers GmMTBa as a critical determinant of salinity stress tolerance

Soybean ( Glycine max ) is an important protein and oil crop whose yield is significantly affected by salinity stress. N 6 -methyladenine (m 6 A), a prominent epigenetic modification of RNA, exerts crucial regulatory functions in plant development and stress responses. Through genome-wide analysis, we identified 55 m 6 A modification–regulatory genes in soybean across 19 soybean chromosomes, categorized into writers, readers, and erasers. The promoters of these genes are enriched in light-, phytohormone-, and stress-responsive cis -elements and display diurnal and tissue-specific expression patterns, suggesting multifaceted regulation. Chromatin immunoprecipitation revealed distinct histone modification signatures associated with these genes, including H3K4me3, H3K36me3, and H2A.Z. Protein–protein interaction analysis confirmed the assembly of core GmMTA–GmMTB–GmFIP37 writer components, with GmFIP37 forming homodimers and heterodimers. Evolutionary analysis showed that GmMTBa underwent strong selection pressure with genetic conservation, while GmMTBb experienced selection during domestication, showing an association with flowering and yield traits. Notably, we discovered that GmMTBa, a core subunit of the m 6 A methyltransferase complex, functions as a critical determinant of salinity stress tolerance in soybean, as Gmmtba mutants exhibited pronounced salinity sensitivity. Mechanistically, GmMTBa regulates the m 6 A modification of GmMSH1 transcripts, a key suppressor of stress signal transduction. GmMSH1 knockdown lines were more tolerant to salinity stress, under which conditions GmMSH1 expression was significantly elevated in Gmmtba mutants. These results indicate that GmMTBa influences salinity stress tolerance by modulating MSH1 -dependent stress signaling pathways. Our findings reveal an m 6 A-mediated regulatory mechanism in plant stress acclimation and establish GmMTBa as a promising candidate for improving soybean resilience to salinity stress.