From endodormancy to ecodormancy: the transcriptional landscape of apple floral buds

Authors: SAPKOTA, SANGEETA - Virginia Tech; SALEM, MOHAMED - Virginia Tech; JAHED, KHALIL - Virginia Tech; Artlip, Timothy - Tim; SHERIF, SHERIF - Virginia Tech

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/22/2023
Publication Date: 7/14/2023
Citation: Sapkota, S., Salem, M., Jahed, K., Artlip, T.S., Sherif, S. 2023. From endodormancy to ecodormancy: the transcriptional landscape of apple floral buds. Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1194244.
DOI: https://doi.org/10.3389/fpls.2023.1194244

Interpretive Summary: Global climate change has disrupted spring phenology in recent years, resulting in an increased risk of frost damage in early blooming apple cultivars. Bud dormancy is a crucial stage in the life cycle of temperate perennials as it directly affects the bud re-growth in spring and flowering time. To identify candidate genes regulating the timing of flowering, this study analyzed transcript expression profiles during the dormancy-regrowth cycle in two apple cultivars; ‘Cripps Pink’ and ‘Honeycrisp’; that represent early- and late-bloom cultivars, respectively. Our findings suggest that despite the number of active pathways during the dormancy-regrowth cycle, the fundamental factors controlling the release of dormancy is a complicated interplay between many factors, mainly during ecodormancy (dormancy maintained by environmental factors such as temperature and daylength). A better understanding of these factors may allow breeding of apples that maintain desired consumer characteristics, but later bloom, thus avoiding erratic spring frosts.

Technical Abstract: This study endeavors to explore the transcriptomic profiles of two apple cultivars, namely, 'Honeycrisp' and 'Cripps Pink,' which represent late and early-blooming cultivars, respectively. Using RNA-sequencing technology, we analyzed floral bud samples collected at five distinct time intervals during both endodormancy and ecodormancy. To evaluate the transcriptomic profiles of the 30 sequenced samples, we conducted principal component analysis (PCA). PC1 explained 43% of the variance, separating endodormancy and ecodormancy periods, while PC2 explained 16% of the variance, separating the two cultivars. The number of differentially expressed genes (DEGs) increased with endodormancy progression and remained elevated during ecodormancy. We identified a total of 8504 upregulated and 11634 downregulated DEGs in the comparison of endodormancy and ecodormancy, regardless of cultivar, and 2918 upregulated and 3368 downregulated DEGs in the comparison of 'Honeycrisp' versus 'Cripps Pink,' regardless of dormancy stage. Furthermore, we conducted a co-expression network analysis to gain insight into the coordinated gene expression profiles across different time points, dormancy stages, and cultivars. This analysis revealed the most significant module (ME 14), correlated with 1000 GDH and consisting of 1162 genes. The expression of the genes within this module was lower in 'Honeycrisp' than in 'Cripps Pink.' The majority of the DEGs from ME 14 were primarily related to jasmonic acid biosynthesis and signaling, lipid metabolism, oxidation-reduction, and transmembrane transport activity. This suggests a plausible role for these pathways in governing bud dormancy and flowering time in apple.