SlNF-YC9 coordinates NF-Y trimer assembly and SlWRKY16-mediated antagonism to regulate drought tolerance in tomato

Drought stress severely constrains tomato productivity, yet the transcriptional circuitry governing drought adaptation remains incompletely understood. Here, we demonstrate that SlNF-YC9 assembles with SlNF-YB3b and SlNF-YA3a into a functional NF-Y heterotrimer that enhances drought tolerance. This complex promotes stomatal closure, limits reactive oxygen species accumulation, and elevates abscisic acid levels. Mechanistically, the NF-Y trimer directly activates the drought-responsive genes SlAREB1 and SlDREB2 by binding the CCAAT motif, with SlNF-YA3a mediating DNA contact and the intact complex conferring maximal transcriptional activation. Notably, this activity is antagonized by SlWRKY16, which physically interacts with SlNF-YC9 and suppresses NF-Y-dependent transcription. Genetic analyses further support the cooperative function of SlNF-YC9 and SlNF-YB3b, as well as the antagonistic role of SlWRKY16, in regulating drought tolerance. Together, our findings define the NF-Y complex as a key regulatory component that coordinates positive and negative transcriptional inputs during the tomato drought response, providing a molecular framework for targeted crop improvement.