Columnar-shaped apple (Malus × domestica Borkh.) trees are of interest because of their profitable and labour-saving characteristics based on high-density planting and robotic technologies. Recent studies have shown that the Co gene, which is responsible for the columnar shape, and MdPG1, which contributes to fruit storability and flesh texture, are located on chromosome 10 of the apple genome. In silico analysis and genotypic characterisation of our columnar breeding materials revealed that the unfavourable haplotype carrying both Co and the MdPG1-3 allele that confers low storability was retained in almost all of our current and historical columnar materials because of the strong linkage between the two genes. To overcome this limitation, we conducted large-scale marker-assisted selection to obtain plants harbouring a favourable haplotype conferring a columnar tree with improved storability, and high-quality flesh resulting from recombination events between these genes during meiosis. Large-scale marker-assisted selection of approximately 15,000 seedlings composed of five crosses resulted in the identification of 80 individuals harbouring the targeted recombinant haplotype. These individuals are valuable for breeding columnar apple cultivars with superior fruit quality.