This study explores the mechanism of columnar tree formation in apples and its chemical regulation. Apple production in Japan is declining due to an aging workforce and labor-intensive tasks like pruning and harvesting. The columnar tree shape offers a potential solution by enabling compact growth, simplifying pruning, and allowing mechanized harvesting. The columnar shape originated from a natural mutation in McIntosh Wijcik. Genetic studies identified the Co gene as its key effector, with MdDOX-Co, which is a dioxygenase family enzyme, playing a crucial role. While normally expressed in roots, MdDOX-Co is also expressed in aerial parts in columnar apples, leading to abnormal growth. It inhibits gibberellin (GA) activation by hydroxylating GA at the C-12 position, causing shorter internodes and dwarfism. A chemical screening approach identified C4 as a selective MdDOX-Co inhibitor, allowing potential chemical control of tree morphology. This research contributes to the development of new apple varieties, such as Benitsurugi, introduced in 2024. By regulating MdDOX-Co, fruit coloration and yield may be further improved. These findings could also be applied to other fruit trees, offering a new strategy for enhancing productivity and sustainability in modern agriculture.