Time-Resolved Analysis of Candidate Gene Expression and Ambient Temperature During Bud Dormancy in Apple

Identifying indicators of apple bud dormancy status by exposure to artificial forcing conditions

Dormancy in temperate fruit trees is a mechanism of temporary growth suspension, which is vital for tree survival during winter. Studies on this phenomenon frequently employ scientific methods that aim to detect the timing of dormancy release. Dormancy release occurs when trees have been exposed to sufficient chill, allowing them to resume growth under conducive conditions. This study investigates dormancy dynamics in two apple (Malus × domestica Borkh.) cultivars, 'Nicoter' and 'Topaz', by sampling branches in an orchard over 14 weeks (2019 to 2020) and over 31 weeks (2021 to 2022) and subjecting them to a 42-day budbreak forcing period in a growth chamber. Temporal changes in budbreak percentages demonstrated dormancy progression in the studied apple cultivars and allowed the three main dormancy phases to be distinguished: paradormancy (summer dormancy), endodormancy (deep dormancy) and ecodormancy (spring dormancy), along with transition periods between them. Using these data, we explored the suitability of several alternative methods to determine endodormancy release. Tabuenca's test, which predicts dormancy release based on the differences in dry weights of buds with and without forcing, showed promise for this purpose. However, our data indicated a need for considerable adjustments and validation of this test. Bud weight and water content of buds in the orchard did not align with budbreak percentages under forcing conditions, rendering them unsuitable for determining endodormancy release in 'Nicoter' and 'Topaz'. Shoot growth cessation did not seem to be connected with either dormancy progression or dormancy depth of the studied cultivars, whereas leaf fall coincided with the beginning of the transition from endo- to ecodormancy. This work addresses methodological limitations in dormancy research and suggests considering the mean time to budbreak and budbreak synchrony as additional criteria to assess tree dormancy status.

Functional evidence on the involvement of the MADS-box gene MdDAM4 in bud dormancy regulation in apple

Over the course of the year, temperate trees experience extremes in temperature and day length. In order to protect themselves from frost damage in winter, they enter a dormant state with no visible growth where all leaves are shed and buds are dormant. Also the young floral tissues need to withstand harsh winter conditions, as temperature fruit trees like apple develop their flower buds in the previous year of fruit development. So far, the genetic control of induction and release of dormancy is not fully understood. However, the transcription factor family of DORMANCY-Associated MADS-box (DAM) genes plays a major role in the control of winter dormancy. One of these genes is MdDAM4. This gene is expressed in the early phase of bud dormancy, but little is known about its function. Six transgenic apple lines were produced to study the function of MdDAM4 in apple. For plant transformation, the binary plasmid vector p9oN-35s-MdDAM4 was used that contains the coding sequence of MdDAM4 driven by the 35S promoter. Transgenicity of the lines was proven by PCR and southern hybridization. Based on siRNA sequencing and phenotypic observations, it was concluded that line M2024 overexpresses MdDAM4 whereas the gene is silenced in all other lines. Phenotyping of the transgenic lines provided evidence that the overexpression of MdDAM4 leads to an earlier induction and a later release of dormancy. Silencing this gene had exactly the opposite effects and thereby led to an increased duration of the vegetation period. Expression experiments revealed genes that were either potentially repressed or activated by MdDAM4. Among the potentially suppressed genes were several homologs of the cytokinin oxidase 5 (CKX5), five LOX homologs, and several expansins, which may indicate a link between MdDAM4 and the control of leaf senescence. Among the potentially activated genes is MdDAM1, which is in line with observed expression patterns during winter dormancy. MdDAM2, which shows little expression during endodormancy also appears to be activated by MdDAM4. Overall, this study provides experimental evidence with transgenic apple trees for MdDAM4 being an important regulator of the onset of bud dormancy in apple.

Target enrichment sequencing coupled with GWAS identifies MdPRX10 as a candidate gene in the control of budbreak in apple

The timing of floral budbreak in apple has a significant effect on fruit production and quality. Budbreak occurs as a result of a complex molecular mechanism that relies on accurate integration of external environmental cues, principally temperature. In the pursuit of understanding this mechanism, especially with respect to aiding adaptation to climate change, a QTL at the top of linkage group (LG) 9 has been identified by many studies on budbreak, but the genes underlying it remain elusive. Here, together with a dessert apple core collection of 239 cultivars, we used a targeted capture sequencing approach to increase SNP resolution in apple orthologues of known or suspected A. thaliana flowering time-related genes, as well as approximately 200 genes within the LG9 QTL interval. This increased the 275 223 SNP Axiom® Apple 480 K array dataset by an additional 40 857 markers. Robust GWAS analyses identified MdPRX10, a peroxidase superfamily gene, as a strong candidate that demonstrated a dormancy-related expression pattern and down-regulation in response to chilling. In-silico analyses also predicted the residue change resulting from the SNP allele associated with late budbreak could alter protein conformation and likely function. Late budbreak cultivars homozygous for this SNP allele also showed significantly up-regulated expression of C-REPEAT BINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception, compared to reference cultivars, such as Gala. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signaling and CBF gene regulation. Moving forward, this provides a focus for developing our understanding of the effects of temperature on flowering time and how redox processes may influence integration of external cues in dormancy pathways.

Exploring epigenetic variation for breeding climate resilient apple crops

Climate change with warmer winter and spring temperatures poses major challenges to apple fruit production. Long-term observations confirm the trend toward earlier flowering, which leads to an increased risk of frost damage. New breeding strategies are needed to generate cultivars that are able to stay largely unaffected by warmer temperatures. Recently, epigenetic variation has been proposed as a new resource for breeding purposes and seems suitable in principle for apple breeding. However, to serve as a new resource for apple breeding, it is necessary to clarify whether epigenetic variation can be induced by the environment, whether it can create phenotypic variation, and whether this variation is stable across generations. In this brief review, we summarize the impact of climate change on the timing of apple phenology, highlight how epigenetic variation can potentially support novel breeding strategies, and point out important features of epigenetic variation that are required for its application in breeding programs.