A transcriptome analysis of two apple (Malus × domestica) cultivars with different flowering abilities reveals a gene network module associated with floral transitions

Young 'Nagafu No. 2′ apple trees produce fewer flower buds than the trees of other apple cultivars, including 'Yanfu No. 6′ (i.e., 'Fuji' apple tree exhibiting a bud mutation). Thus, we analyzed the flowering characteristics of these two varieties to further characterize apple floral transition. RNA sequencing was used to characterize differentially expressed genes in buds between the two cultivars during floral transition. Differences in several physiological parameters were also analysed. A total of 3,010, 1,139, and 1346 differentially expressed genes were identified at 30, 50, and 70 days after full bloom. These genes combined with the differences in physiological indices indicated that low gibberellic acid levels and high cytokinin levels in 'Yanfu No. 6′ buds during the floral induction stage increased the production of flower buds. High cytokinin levels inhibited gibberellic acid signaling and promoted floral transition. Additionally, low gibberellic acid levels likely inhibited shoot elongation by impairing DELLA degradation. Meanwhile, relatively high indole-3-acetic acid and cytokinin levels synergistically maintained meristem activities and accelerated bud growth. Moreover, the high sucrose content in 'Yanfu No. 6′ buds up-regulated the transcription of TREHALOSE 6-PHOSPHATE SYNTHASE and SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes, which ultimately promoted floral induction. The data presented herein indicate that floral transition differences between the two analyzed apple cultivars are linked to sugar and cytokinin signaling pathways.