Chilling stress is a major threat to rice and other plants of subtropical and tropical origins. Identifying chilling tolerance genes and their mechanisms are key to improve plant performance under chilling. A GWAS study of chilling tolerance variation in Indica rice identified OsCTK1 that codes for a casein kinase as a causal gene. OsCTK1 positively regulate rice chilling tolerance. A natural OsCTK1 CT variant exhibits a higher kinase activity and confers greater chilling tolerance compared to a CS variant. This CT variant is distributed more frequently in higher latitude compared with the CS variant, suggesting a local adaptation of variants. Phosphoproteomics identified a number of putative substrates of OsCTK1, including acidic ribosomal protein OsP3B, cyclic nucleotide-gated ion channel OsCNGC9, dual-specific mitogen-activated protein kinase phosphatases OsMKP1, and a SnRK1 protein. Potential new regulation and mechanisms in chilling tolerance are revealed by functional studies of these putative substrates and will be discussed in this presentation.