Wild rice *GL12^W* improves grain length and salt tolerance in both indica and japonica genetic backgrounds. *GL12^W* alters cell length by regulating grain size related genes including *GS2*, and positively regulates salt tolerance related genes, such as *NACs*, *NCED3*, under salt stresses. A G/T variation in the *GL12* promoter determines its binding to coactivator GIF1 and transcription factor WRKY53, impacting expression and contributing to indica/japonica subspecies divergence. The study provides resources for rice breeding and insights into yield and salt tolerance trade-off mechanisms.

Yanyan Wang, Wenxi Chen, Meng Xing, Jiaqiang Sun, Shizhuang Wang, Ziyi Yang, Jingfen Huang, Yamin Nie, Mingchao Zhao, Yapeng Li, Wenlong Guo, Yinting Wang, Ziyi Chen, Qiaoling Zhang, Jiang Hu, Yunhai Li, Ke Huang, Xiaoming Zheng, Leina Zhou, Lifang Zhang, Yunlian Cheng, Qian Qian, Qingwen Yang, Weihua Qiao