Background Bud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during bud dormancy in trees. However, they usually examined bud development or bud dormancy in isolation. In this work, we aimed to further explore the global transcriptional changes happening throughout bud development and dormancy onset, progression and release.Results Using next-generation sequencing and modelling, we conducted an in-depth transcriptomic analysis for all stages of flower buds in several sweet cherry ( Prunus avium L.) cultivars that are characterized for their contrasted dates of dormancy release. We find that buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are defined by the expression of genes involved in specific pathways, and these are conserved between different sweet cherry cultivars. In particular, we found that DORMANCY ASSOCIATED MADS-box (DAM) , floral identity and organogenesis genes are up-regulated during the pre-dormancy stages while endodormancy is characterized by a complex array of signalling pathways, including cold response genes, ABA and oxidation-reduction processes. After dormancy release, genes associated with global cell activity, division and differentiation are activated during ecodormancy and growth resumption. We then went a step beyond the global transcriptomic analysis and we developed a model based on the transcriptional profiles of just seven genes to accurately predict the main bud dormancy stages.Conclusions Overall, this study has allowed us to better understand the transcriptional changes occurring throughout the different phases of flower bud development, from bud formation in the summer to flowering in the following spring. Our work sets the stage for the development of fast and cost effective diagnostic tools to molecularly define the dormancy stages. Such integrative approaches will therefore be extremely useful for a better comprehension of complex phenological processes in many species.*   LIST OF ABBREVIATIONS    :       ABA    :   abscisic acid    ABF2    :   ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR 2    ABI5    :   ABSCISIC ACID INSENSITIVE 5    AG    :   AGAMOUS    AGL9    :   AGAMOUS-like 9    AGL20    :   AGAMOUS-like 20    AP3    :   APETALA3    AREB3    :   ABSCISIC ACID RESPONSE ELEMENT-BINDING PROTEIN 3    ATHB7    :   ARABIDOPSIS THALIANA HOMEOBOX 7    CBF/DREB    :   C-REPEAT/DRE BINDING FACTOR 2/DEHYDRATION RESPONSE ELEMENT-BINDING PROTEIN    CSLG3    :   Cellulose Synthase like G3    DAM    :   DORMANCY ASSOCIATED MADS-box    DEG    :   differentially expressed gene    DNA    :   desoxyribonucleic acid    EE    :   Evening element motif    EF1    :   Elongation factor 1    ERF    :   ethylene-responsive element    FD    :   FLOWERING LOCUS D    FIMO    :   Find Individual Motif occurrences    FLC    :   FLOWERING LOCUS C    GH127    :   Glycosyl Hydrolase 127    GPX6    :   GLUTATHION PEROXIDASE 6    GR    :   GLUTATHION REDUCTASE    GRF7    :   GROWTH-REGULATING FACTOR7    GST8    :   GLUTATHION S-TRANSFERASE8    GO    :   gene ontology    H3    :   Histone 3    LEA    :   LATE EMBRYOGENESIS ABUNDANT PROTEIN    LHY    :   LATE-ELONGATE HYPOCOTYL    LP1    :   LIPID TRANSFER PROTEIN1    MEE9    :   maternal effect embryo arrest 9    Padj    :   adjusted p-value     Pav    :   Prunus avium     PC    :   principal component    PCA    :   principal component analysis    PDCB3    :   PLASMODESMATA CALLOSE-BINDING PROTEIN 3    PIF4    :   PHYTOCHROME INTERACING FACTOR 4    PIL5    :   PHYTOCHROME INTERACING FACTOR 3 LIKE 5    PP2C    :   Phosphatase 2C    RNA    :   ribonucleic acid    RPII    :   ribonucleic acid polymerase II    RT-qPCR    :   quantitative reverse transcriptase polymerase chain reaction    RVE1/8    :   REVEILLE1/8    SEP3    :   SEPALLATA3    SPT    :   SPATULA    SRP    :   STRESS RESPONSIVE PROTEIN    TCX2    :   TESMIN/TSO1-like CXC 2    TF    :   transcription factor    TPM    :   transcripts per million reads    UDP-GalT1    :   UDP-Galactose transporter 1    ZTL    :   ZEITLUPE

From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy