The maize ZmCPK39-ZmKnox2 module regulates plant height

Plant height is an important agronomic trait that affects high-density tolerance and lodging resistance. However, the regulators and their underlying molecular mechanisms controlling plant height in maize remain understudied. Here, we report that knockout mutants of the calcium-dependent protein kinase gene ZmCPK39 (ZmCPK39-KO) exhibit dramatically reduced plant height, characterized by shorter internodes and a slight decrease in node numbers. Furthermore, we identified a ZmCPK39-interacting protein, the knotted-related homeobox (ZmKnox2), and observed that plant height was also significantly reduced in a mutator transposon-inserted mutant of ZmKnox2 (ZmKnox2-Mu). Combined analysis of transcriptomic and metabonomic data indicates that multiple phytohormone signaling and photosynthesis pathways are disrupted in both ZmCPK39-KO and ZmKnox2-Mu mutants. Taken together, these results provide new insights into the function of ZmCPK39 and identify potential targets for breeding lodging-resistant and high-density tolerant maize cultivars.