A Rare Allele of ST5 From Wild Rice Enhances Salt Tolerance in Rice

Soil salinity critically impairs global rice productivity, necessitating the exploration of salt-tolerant genetic resources in wild rice (Oryza rufipogon). Here, we identified a C2H2 transcription factor, ST5, from wild rice using a chromosome segment substitution line population. Functional analysis reveals that ST5 negatively regulates rice salt tolerance. A 36-bp insertion in the ST5^W promoter harbors two W-box motifs, transcription factor OsWRKY80 binds to this insertion and represses ST5^W expression. This repression reduces ST5^W expression, alleviating its negative regulation on the downstream genes OsCPK4, which are pivotal for maintaining Na⁺/K⁺ homeostasis under salinity stress. Notably, the ST5^W allele is exclusively present in a few of O. rufipogon accessions and absent in all cultivated rice varieties. Field trials demonstrate ST5^W significantly improves grain yield across diverse genetic backgrounds under saline field conditions. Our work provides both an underexploited genetic resource and molecular insights for breeding salt-tolerant rice varieties to address soil salinization challenges.