Dormancy is an adaptive mechanism that enables plants to survive unfavorable climatic conditions and allows budbreak and flowering to occur only when the conditions are permissive. This resting stage is defined by the absence of visible growth. In apple (Malus x domestica Borkh.) and many other Rosaceae species, winter bud dormancy can be divided in at least two phases: endo- and eco-dormancy. During endo-dormancy, growth repression is controlled by internal cues and it is released by long periods of cold (chilling requirement). Then, buds undergo into eco-dormancy phase and become competent to budbreak in response to warm temperatures. In the model plant species Arabidopsis thaliana, changes in ambient temperature regulate flowering time through mechanisms that involved the alternative splicing (AS) of MADS-box genes. We have hypothesized that a similar mechanism could operate to control the temperature dependent transition between endo- and eco-dormancy phases in apple tree. In order to address this question, we have performed a RNA-seq time-course experiment on buds of apple tree (cv. Golden delicious) during the dormancy cycle. RNA from time-points covering the endo- to eco-dormancy transition were sequenced and changes in gene expression and AS quantified. Our bioinformatics analyses showed that pathways related to cell wall modifications, cell cycle, chromatin silencing and hormones, among others, were affected during the transition between endo- to eco-dormancy. Moreover, we implemented a bioinformatics pipeline to identify differential alternatively spliced genes associated to this developmental transition. Here, we will show how these data are instrumental to isolate candidate genes potentially involved in dormancy-cycle control and describe mechanisms of post-transcriptional regulation involved in fruit tree development.