Comparative genomics and transcriptomics on salt tolerance of Vigna luteola

Vigna luteola, a wild legume species, shows remarkable variation in salinity tolerance across its natural habitats, with coastal populations exhibiting high tolerance and riverbank populations being sensitive. This intraspecific variation provides a valuable system for investigating the genetic basis of salt tolerance. A major QTL for salt tolerance was previously identified by crossing salt-tolerant and salt-sensitive accessions, but the responsible genes remain unknown. In this study, grafting experiments between the two accessions revealed that the root plays a primary role in salt tolerance by suppressing Na⁺ transport to the shoot. We then conducted root transcriptome analysis and identified four candidate genes located within the QTL and highly expressed under salt stress in the tolerant accession: CBL-INTERACTING PROTEIN KINASE 6 (CIPK6), CAFFEOYL SHIKIMATE ESTERASE (CSE), FCS-LIKE ZINC FINGER PROTEIN 13 (FLZ13), and DROUGHT-INDUCED 21 (DI21). Promoter analysis revealed that the CIPK6 promoter contains transcription factor binding motifs unique to the salt-tolerant accession, which may contribute to its high expression under salt stress. These findings suggest that CIPK6 is regulated by cis-regulatory differences and is the most promising candidate for the salt-tolerance QTL. The identified genes in this study provide a foundation for developing salt-tolerant crops in the future.