Abstract
Temperate and boreal trees face harsh conditions during winter such as extreme cold, drought and insufficient light. These trees have developed a specific mechanism called “bud dormancy” to protect their meristem and floral tissues during winter, and to allow the next growth cycle to occur at an appropriate time in the next spring. Three successive stages are usually considered during dormancy. In this thesis, I focused on two of them, endo and eco-dormancy and on the transition between them. In the endo-dormant stage, bud growth is not possible even when placed under forcing conditions (i.e. warm temperatures). This stage requires exposure to cold temperatures to be overcomed. Then, the buds enter into the ecodormancy stage, in which growth is repressed by not suitable environmental conditions. Once in warmer conditions, the tree opens its buds (budbreak) and enters into the growth and reproductive phase. In this PhD, I have studied dormancy in the apple tree (Malus domestica Borkh), an economically important fruit crop that presents chilling-dependent bud dormancy. The chilling requirements (CR) necessary to overcome endodormancy are known to vary among cultivars. CR are thus genetically defined and genes as DORMANCY ASSOCIATED MADS-box genes (DAMs) have been reported as main dormancy regulators. In Arabidopsis thaliana, MADS-box genes act in the vernalization and the thermosensory pathways to control flowering time in response to ambient temperature. These pathways are partly modulated at the transcriptional and post-transcriptional levels. At the post-transcriptional level, alternative splicing (AS) mechanisms and microRNAs (miRNAs) are known to operate in the temperature-mediated control of flowering in A. thaliana. In this Thesis, my working hypothesis is that the temperature-mediated regulation of dormancy and budbreak in apple (and other fruit trees) is regulated by similar mechanisms to those that operate in the vernalization and thermosensory flowering pathways of A. thaliana. Thus, I investigated differentially expressed genes and miRNAs during endormancy and transition to ecodormancy, and I performed a preliminary analysis to detect alternative splicing (AS) events to better understand the post-transcriptional regulation of dormancy in apple tree. Using a transcriptomic approach, I performed RNA and small RNA sequencing analysis to study the differential expression of genes and miRNAs during endodormancy release and transition to ecodormancy. This highlighted a huge reprograming in gene expression during this dormancy switch, with a high number of genes being up-regulated during endodormancy release. We detected two isoforms of AS for the dormancy-related Malus domestica (Md) gene SHORT VEGETATIVE PHASE a (MdSVPa) with potentially different functions. Moreover, the expression of some of the dormancy associated genes were sensitive to temperature variation and/or Reactive Oxidative Species (ROS). Furthermore, two cultivars of apple trees with different chilling requirements presented different gene expression, especially in the apple homologs of the A. thaliana HOMEOBOX PROTEIN 22 (HB22) and AINTEGUMENTA (ANT) genes. Among the detected miRNAs, we could identify 17 that were differentially expressed during endodormancy release. In particular, the expression pattern of miR159a suggests a role of this miRNA during dormancy linked to the abscisic acid perception. This work brings new knowledge on the role of AS and miRNAs in bud dormancy post-transcriptional regulation even though more studies are necessary to fully understand their impact in such complex mechanisms as bud dormancy.