Integrated physiological and transcriptomic analyses uncover mechanisms regulating axillary bud outgrowth in apple

• Axillary bud outgrowth differs between ‘VG’ and ‘HS’ apple cultivars. • Sucrose and cytokinin levels are higher in axillary buds of easy-to-branch ‘VG’. • Hard-to-branch ‘HS’ axillary buds accumulate higher ABA, JA, and SL. • Transcriptome analysis identifies more than 3000 DEGs between ‘VG’ and ‘HS.’ • Some DEGs are involved in sugar metabolism and hormone signalling. Shoot branching in apple ( Malus domestica ) is primarily affected by the activation and outgrowth of axillary buds, which are regulated by a complex interplay of physiological and genetic factors. To gain deeper insight into the underlying regulatory mechanisms, we compared the physiological characteristics and transcriptomic profiles of two apple cultivars with different branching behaviours: ‘Venus Gold’ (VG, easy-to-branch) and ‘Huashuo’ (HS, hard-to-branch). Physiological assays revealed higher sucrose and cytokinin levels in ‘VG’, while ‘HS’ had higher abscisic acid, jasmonic acid, and strigolactones, which generally inhibit axillary bud outgrowth. Transcriptomic analysis identified 3022 differentially expressed genes, with ‘VG’ showing upregulation of pathways related to sugar metabolism, cytokinesis, and cell wall biogenesis, and ‘HS’ enriched in genes involved in meristem maintenance and stress responses. Our findings provide insights into the physiological and genetic regulation of shoot branching in apple and offer valuable targets for breeding programs of shoot architecture optimization.