Identification and functional characterization of <i>STG5.2</i> conferring salt tolerance in rice

Jie Ma; Yilin Li; Hongshuang Jiang; Qiang Xu; Shaomin Shi; Xueke Chen; Zhipeng Zhang; Danlin Huang; Ying Wang; Huiying He; Chongke Zheng; Lianguang Shang; Xianzhi Xie; Jingguang Chen; Hua Wei

doi:10.1016/j.jgg.2026.04.001

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

doi: 10.1016/j.jgg.2026.04.001

a. School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China;
b. State Key Laboratory of Genome and Multi-omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China;
c. College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China;
d. Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China;
e. National Center of Technology Innovation for Comprehensive Utilization of Saline-AlkaliLand, Dongying, Shandong 250700, China

Funds:

D Program of China (2024YFF1000400), Key R&

D Program of Shandong Province, China (2023LZGC021), the National Natural Science Foundation of China (32522075, 32502020), the Science and Technology Innovation Project of the Shandong Academy of Agricultural Sciences (CXGC2025H08).

This research was supported by National Key R&

Received Date: 2026-02-13
Accepted Date: 2026-04-01
Rev Recd Date: 2026-04-01

Available Online: 2026-04-09

Abstract

Abstract

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 (GWAS) and expression quantitative trait locus (eQTL) 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 modulates 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.
- Rice,
- GWAS,
- Natural variation,
- Salt tolerance,
- Ion homeostasis

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References(53)

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