The NAC transcription factor ClNAC100 positively regulates plant height and fruit size in watermelon

Fruit size correlates with yield potential and serves as a vital agronomic trait. However, the key regulatory genes controlling fruit size in watermelon (Citrullus lanatus) remain poorly understood. In this study, we identified a NAC transcription factor gene ClNAC100 localized to selective sweep regions that positively regulated plant height and fruit size. CRISPR-Cas9-mediated knockout of ClNAC100 caused dramatic reductions in both plant height and fruit size, concomitant with decreased gibberellin (GA) levels in mutants. Exogenous GA₄ application partially rescued the plant height and fruit size of the clnac100 mutant, while it could not restore these traits to wild-type levels. ClNAC100 directly upregulated expansin gene ClEXPA1 and GA biosynthetic genes ClGA3oxs, though DELLA protein interactions attenuated this transcriptional activation. A natural variant (−1087, T/C) of ClNAC100 enabled the Dof transcription factor ClDof4.6 to bind and activate ClNAC100 expression during watermelon domestication. Together, our results demonstrate that ClNAC100 mainly modulates the GA pathway to regulate fruit size and plant height, advancing mechanistic understanding of these agriculturally critical traits.