Natural Variation in a Type-A Response Regulator Gene Confers Maize Chilling Tolerance

Maize (Zea mays L.) is a cold-sensitive species that often faces chilling stress, which adversely affects growth and reproduction. However, the genetic basis of low-temperature adaptation in maize is unclear. Here, we demonstrate that natural variation in the type-A Response Regulator 1 (ZmRR1) gene leads to differences in chilling tolerance among maize inbred lines. Association analysis revealed that InDel-35 of ZmRR1, encoding a protein harboring a mitogen-activated protein kinase (MPK) phosphorylation residue, is strongly associated with chilling tolerance. ZmMPK8, a negative regulator of chilling tolerance, interacts with and phosphorylates ZmRR1 at Ser15. The deletion of a 45-bp region of ZmRR1 harboring Ser15 inhibits its degradation via the 26S proteasome pathway by preventing its phosphorylation by ZmMPK8. Transcriptome analysis indicated that ZmRR1 positively regulates ZmDREB1 and CesA gene expression to enhance chilling tolerance. Our findings thus provide a potential genetic resource for modifying chilling tolerance traits in crops.