Transcriptome analysis uncovers salt stress-responsive mechanisms and GmCML48 as a key candidate gene in soybean

• Transcriptomic analysis reveals the differences among genotypes and tissues in salt response. • Significant enrichment differences in the plant-pathogen interaction pathway were observed between salt-tolerant variety Q and salt-sensitive variety D. • GmCML4 8 exhibits high expression levels in roots and is potently induced by NaCl, NaHCO₃, ABA, and BR. • GmCML48 improves growth and antioxidant enzyme activities to enhance salt tolerance. • Haplotype analysis identifies Hap_A as the superior salt-tolerant haplotype of GmCML48 . Salt stress severely affects soybean yield and cultivation area. A comprehensive understanding of the molecular mechanisms underlying soybean response to salinity is essential for the development of salt-tolerant cultivars. In this study, transcriptome profiling was employed to compare salt-sensitive (D) and salt-tolerant (Q) variety by analyzing the leaf and root tissues under salt stress. A total of 6,276 and 3,278 differentially expressed genes (DEGs) were identified in the leaves and roots of salt-tolerant variety Q, whereas 9,761 and 11,875 DEGs were detected in salt-sensitive variety D, respectively. The regulatory pathways activated under salt stress exhibited significant differences between genotypes and tissues. The plant hormone signal transduction pathway was strongly activated in both tissues of both cultivars, with key genes in multiple hormone pathways demonstrating substantially higher transcriptional upregulation in the salt-tolerant variety Q. Notably, the activation level of the plant-pathogen interaction pathway differed greatly between varieties, with the GmCML gene family accounting for a major proportion of this pathway. Comparative analysis identified GmCML48 as the gene most strongly induced by NaCl, NaHCO 3 , ABA, and BR treatments. Transgenic overexpression lines displayed significant improvements in growth traits and antioxidant enzyme activities under salt stress, establishing GmCML48 as a key contributor to soybean salt tolerance. Furthermore, Hap_A was identified as a haplotype associated with superior salt tolerance. These findings could advance the understanding of soybean molecular adaptations to saline environments and provide a theoretical basis for targeted breeding of salt-tolerant cultivars.