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

ABSTRACT 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.