BackgroundBud 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.ResultsUsing 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.ConclusionsOverall, 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.

18Background. Bud dormancy is a crucial stage in perennial trees and allows survival over winter to 19 ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular 20 events occurring during bud dormancy in trees. However, they usually examined bud development or 21 bud dormancy in isolation. In this work, we aimed to further explore the global transcriptional changes 22 happening throughout bud development and dormancy onset, progression and release. 23Results. Using next-generation sequencing and modelling, we conducted an in-depth transcriptomic 24 analysis for all stages of flower buds in several sweet cherry (Prunus avium L.) cultivars that are 25 characterized for their contrasted dates of dormancy release. We find that buds in organogenesis, 26 paradormancy, endodormancy and ecodormancy stages are defined by the expression of genes 27 involved in specific pathways, and these are conserved between different sweet cherry cultivars. In 28 particular, we found that DORMANCY ASSOCIATED MADS-box (DAM), floral identity and 29 organogenesis genes are up-regulated during the pre-dormancy stages while endodormancy is 30 characterized by a complex array of signalling pathways, including cold response genes, ABA and 31 oxidation-reduction processes. After dormancy release, genes associated with global cell activity, 32 division and differentiation are activated during ecodormancy and growth resumption. We then went 33 a step beyond the global transcriptomic analysis and we developed a model based on the transcriptional 34 profiles of just seven genes to accurately predict the main bud dormancy stages. 35Conclusions. Overall, this study has allowed us to better understand the transcriptional changes 36 occurring throughout the different phases of flower bud development, from bud formation in the 37 summer to flowering in the following spring. Our work sets the stage for the development of fast and 38 cost effective diagnostic tools to molecularly define the dormancy stages. Such integrative approaches 39 will therefore be extremely useful for a better comprehension of complex phenological processes in 40 many species. 41 42 KEY WORDS: Transcriptomic, RNA sequencing, time course, Prunus avium L., prediction, seasonal 43 timing 44 45 BACKGROUND 46 Temperate trees face a wide range of environmental conditions including highly contrasted 47 seasonal changes. Among the strategies to enhance survival under unfavourable climatic conditions, 48bud dormancy is crucial for perennial plants since its progression over winter is determinant for 49 optimal growth, flowering and fruit production during the subsequent season. Bud dormancy has long 50 been compared to an unresponsive physiological phase, in which metabolic processes within the buds 51 are halted by cold temperature and/or short photoperiod. However, several studies have shown that 52 bud dormancy progression can be affected in a complex way by temperature, photoperiod or both, 53 depending on the tree species [1][2][3][4][5]. Bud d...