Identification and functional characterization of STG5.2 conferring salt tolerance in rice

Saline-alkaline stress severely constrains rice productivity, posing a critical threat to global food security. Identifying uncharacterized salt-tolerance genes with agronomic value is therefore essential for breeding stress-resilient and high-yield rice varieties. In this study, we identify a previously unidentified gene, LOC_Os05g07260, by combining genome-wide association study and expression quantitative trait locus mapping, and designated it as Salt Tolerance Gene 5.2 (STG5.2), which encodes a phosphatidylinositol glycan-related protein. Functional validation reveals that STG5.2 acts as a positive regulator of both salt stress tolerance and yield-related traits in rice. STG5.2 may reprogram metabolic pathways and regulate the expression of salt-responsive genes including Na⁺ exclusion-related Salt Overly Sensitive 1 (OsSOS1), High-Affinity K⁺Transporter 2;1 (OsHKT2;1), and stress tolerance-positive regulator Acireductone Dioxygenase 1 (OsARD1), forming a multi-layered regulatory network for salt adaptation. Combined with phenotypic data from chromosome segment substitution lines, the superior STG5.2 haplotype, predominantly present in indica rice, shows great potential for improving salt tolerance in japonica backgrounds. Overall, our results highlight that STG5.2 may modulate rice salinity resilience by regulating ion homeostasis and the coordination of multiple stress-responsive pathways, providing a potential molecular basis for salt-tolerant rice varieties breeding.