Epigenetics provides plants with a way to survive tough weather conditions by inducing a state of bud dormancy. Changes in environmental conditions or internal signals prompt the buds to switch between active growth and dormancy. Researchers are investigating how chromatin structure and transcriptional changes in buds contribute to this process, using artificial intelligence models to analyze their data. The results of this study underscore the role of epigenetic strategies in helping plants withstand shorter winters due to global warming.
Plants have evolved to survive in challenging environments. A plant’s winter bud is essential for its ability to adapt. Buds can shift between growth and dormancy based on external conditions and internal signals. There are three phases of dormancy, which are triggered by specific signals: ecodormancy, influenced by the environment; paradormancy, caused by signals from other parts of the plant; and endodormancy, driven by internal signals within the bud. Buds in paradormancy enter endodormancy in response to changes in day length or lower temperatures in the fall, while the endo- and eco-dormant stages occur when exposed to chilling temperatures. Transitioning from para- to endodormancy serves as a protective measure for the bud. However, the epigenetic processes that lead to endodormancy have not been thoroughly studied.
A new study published in Tree Physiology on June 21, 2024, by Assistant Professor Takanori Saito and his team investigates the epigenetic alterations in chromatin and transcriptional shifts that facilitate temperature detection in ‘Fuji’ apple axillary buds. Their findings were further analyzed using deep-learning AI models alongside statistical methods. Dr. Shanshan Wang, Dr. Katsuya Ohkawa, Dr. Hitoshi Ohara, and Dr. Satoru Kondo from Chiba University’s Graduate School of Horticulture co-authored this research.
One goal of this study was to identify differentially expressed genes (DEGs) during the transition from para- to endodormancy. During the initial stages of bud dormancy, genes involved in responses to low oxygen, defense mechanisms against abscisic acid (ABA), and circadian rhythms became active. The authors also found that nucleosome depletion did not correlate with the transcription patterns observed. “Interestingly, while a shift in nucleosome positions in the presumed promoter regions was noted among the DEGs, we did not observe significant differences in nucleosome occupancy for most gene bodies during the dormancy transition of the axillary bud,” explains Dr. Saito.
Cis-regulatory elements (CREs), which are short sequences of DNA that impact gene expression, were also examined. The researchers analyzed the connection between transcriptional changes and CREs using a deep-learning AI model. Dr. Saito elaborated, “We identified CREs linked to the cell cycle, circadian rhythm, and the TATA box. Notably, the significance of circadian rhythms for downregulated genes was consistent with the observed transcriptional changes.” Additionally, the data suggested that the COL9 signal might play a role in modifying CO levels to induce bud dormancy.
Whereas many AI-driven epigenetic studies rely on extensive datasets, this research utilized a smaller dataset. Nevertheless, Bayesian statistical analysis connected epigenetic alterations to gene transcription related to winter bud regulation. The AI approach utilized in this study has the potential to advance epigenetic analysis, particularly for non-model plants with less comprehensive genomic information.
Dr. Saito noted that “Our comprehensive results using deep learning indicate that the cold-modulated circadian rhythm-based system for inducing dormancy in axillary buds is regulated by single-nucleosome fluctuations.”
In the future, these discoveries could lead to more effective methods for ensuring sustainable cultivation of crops, plants, and trees in response to the challenges posed by global warming.
