Xiaoli Chen , Yulong Ren, Hui Dong, Xiaokang Jiang, Xiaoming Zheng, Erchao Duan, Xuan Teng, Yunlong Wang, Chuanwei Gu, Rongbo Chen,Qingkai Wang, Yongfei Wang, Yipeng Zhang, Rushuang Zhang,Yunpeng Zhang, Wenjie Zhao, Yu Zhang, Xue Yang, Lei Zhou, Chao Li, Tiaofeng Shan, Yiqun Bao, Yunlu Tian, Xi Liu, Shijia Liu, Tao Guo, Mingjiang Chen, Haiyang Wang, Yihua Wang, Jianmin Wan

Nature Genetics; 2025; IF: 29

DOI:10.1038/s41588-025-02429-2

Abstract

Chalkiness and seed vigor are major agronomic traits affecting rice grain quality and productivity, respectively. Little is known about the intrinsic relationship and the regulatory mechanisms of these two traits. Here we identified a chalkiness locus qPGWC-8, which encodes trehalose-6-phosphate synthase 8 (OsTPS8) that suppresses trehalose-6-phosphate(Tre6P) biosynthesis by interacting with and inhibiting OsTPS1. A natural promoter variation in OsTPS8 confers differential transcriptional regulation by OsbHLH001. Elevated expression of OsTPS8 reduces Tre6P levels and activates the expression of OsMYBS1 and α-amylase genes, thus promoting starch degradation, chalkiness formation and seed vigor elevation. Two major haplotypes, OsTPS8^ASO and OsTPS8^IR24, were defined by this functional promoter variation, with OsTPS8^IR24 preferentially selected during the domestication of indica rice. Collectively, our findings establish an OsbHLH001-OsTPS8-Tre6P-α-amylase signaling cascade that has a dual role in regulating grain chalkiness and seed vigor, which reveals a molecular link between the appearance quality and seed vigor of rice.