Natural variation in the COT1 promoter improves rice seedling cold tolerance by OsCBF3-dependent transcriptional activation

Low-temperature stress is a major constraint to global rice production. Identifying novel genetic resources to enhance cold tolerance is critical for achieving rice high- and stable-yield. Here, we cloned a quantitative trait locus (COT1) conferring cold tolerance at the seedling stage in common wild rice (Oryza rufipogon), which encodes an AN1-like zinc finger domain protein. We demonstrated that natural variation in the COT1 promoter region modulates its transcriptional activation by OsCBF3, thereby regulating COT1 expression and seedling cold tolerance. Furthermore, COT1 enhances cold tolerance by promoting CK2β3 degradation, which increases phosphorus accumulation and improves photosynthetic efficiency under cold stress. These findings not only offered new insights into the molecular mechanism of seedling cold tolerance, but also provided valuable genetic resources for improving cold tolerance in rice.