Transcriptome analysis and genome-wide identification of WD40 transcription factor family provide new insights into the salt tolerance of Melilotus albus

Salt stress is one of the major factors limiting the growth and yield of Melilotus albus , a legume valued for its high protein content, medicinal coumarins, and salinity tolerance. To investigate the molecular basis of salt adaptation, we conducted a time-course transcriptome analysis under prolonged salt stress (0, 7, 14, and 21 d), combined with phenotypic and physiological measurements. Transcriptome profiling, WGCNA, and STEM analyses identified differentially expressed genes enriched in stress-response pathways, with members of the WD40 transcription factor family exhibiting particularly notable salt-responsive expression patterns. We identified WD40 genes at the genome-wide level and characterized their promoter structures, chromosomal distributions, and evolutionary relationships. Three members (MaWD40.16, MaWD40.45, and MaWD40.116) were further validated for their expression patterns by qRT-PCR and tissue-specific analysis, which confirmed their preferential expression in roots. Functional assays, including yeast complementation, subcellular localization, and analyses of transgenic hairy root lines, demonstrated that the encoded proteins are localized in the nucleus and enhance salt tolerance. In addition, they modulate physiological traits such as root length, MDA, and Pro content under stress. Together, these findings highlight the role of MaWD40 genes in salt-stress adaptation and provide a foundation for future functional characterization and molecular breeding of M. albus . • Physiological and transcriptomic evidence of salt tolerance in Melilotus albus was revealed. • Genome-wide identification of 195 MaWD40 transcription factors in Melilotus albus . • Time-course transcriptome profiling revealed salt-responsive DEGs and WD40 candidates. • MaWD40.16 , MaWD40.45 , and MaWD40.116 were nuclear-localized and enhanced salt tolerance in yeast and hairy roots. • Findings provide molecular insights and candidate genes for breeding salt-tolerant legumes.