Molecular characterization of flower bud dormancy under constrained temperatures unveils a shallow dormancy stage induced by cold deprivation

Mild winters are becoming increasingly common in temperate regions due to climate change, which may have important impacts on ecosystems and agriculture. In particular, rising temperatures affect the progression of winter dormancy—a crucial developmental stage in perennial plants—making tree development and reproduction particularly vulnerable to climate change. A better understanding of how future temperature conditions will disrupt dormancy in cultivated fruit trees is crucial for anticipating the impeding consequences and identifying potential adaptation strategies. We investigated the effect of very constrained temperature conditions, i.e. several levels of cold deprivation and early cold exposure, on sweet cherry flower buds during dormancy onset and maintenance, using phenological observations and transcriptomic analyses. We show that temperature is a major driver of dormancy progression as cold deprivation and early cold exposure strongly modify the timing of phenological phases as well as gene expression patterns. We identified genes and signaling pathways specifically activated and/or repressed by cold temperatures, and therefore potentially involved in the optimal progression of dormancy. Finally, thanks to an integrative analysis of molecular data obtained under natural and prolonged warm conditions, we characterize a distinct shallow dormancy phase induced by cold deprivation, with a unique molecular signature. Highlights Our phenological and molecular analysis of sweet cherry dormancy under constrained conditions reveals a gene expression timeline in response to temperature and uncovers a shallow dormancy stage induced by cold deprivation.