Leaf coloration in plants is largely determined by anthocyanins, a class of flavonoid pigments that also contribute to stress tolerance and environmental adaptation. In many ornamental species, leaf color changes dramatically across seasons, but the regulatory logic linking environmental signals to pigment biosynthesis is still unclear. Previous studies have identified individual transcription factors involved in anthocyanin production, yet how these regulators are coordinated at the chromatin and epigenetic levels during seasonal transitions remains unresolved. Moreover, the role of three-dimensional genome organization and DNA methylation in shaping pigment dynamics has been largely unexplored. Based on these challenges, there is a clear need to investigate the integrated regulatory mechanisms governing seasonal leaf color transitions.
In a study published (DOI: 10.1093/hr/uhaf257) online in Horticulture Research in January 2026, researchers from the Anhui Academy of Agricultural Sciences and collaborating institutions report a comprehensive molecular framework explaining seasonal leaf color changes in Japanese maple (Acer palmatum). Using a multi-omics strategy that combines metabolomics, RNA sequencing, chromatin accessibility mapping, DNA methylation profiling, and three-dimensional genome analysis, the team uncovers how specific transcription factors and epigenetic features jointly regulate pigment accumulation, driving the recurring red–green–red leaf transitions observed across spring, summer, and autumn.
The researchers focused on Acer palmatum ‘Duocai’, a cultivar that displays red leaves in spring and autumn but turns green in summer. Metabolomic profiling revealed that cyanidin-3-O-glucoside is the dominant anthocyanin associated with red leaf coloration, showing dramatic seasonal fluctuations. Transcriptomic analyses further identified coordinated changes in genes involved in anthocyanin biosynthesis, closely matching pigment accumulation patterns.
By integrating chromatin accessibility, DNA methylation, and Hi-C data, the study demonstrated that anthocyanin-related genes are tightly regulated by epigenomic remodeling. Among these, ApMYB2 emerged as a central transcription factor controlling pigment biosynthesis by directly activating ApF3'H2, a key enzyme in the cyanidin pathway. Functional experiments confirmed that overexpression of ApMYB2 increased anthocyanin levels, while gene silencing produced the opposite effect.
Crucially, the study uncovered a dual regulatory mechanism upstream of ApMYB2. The transcription factor ApWRKY26 acts as a positive regulator, enhancing ApMYB2 expression during spring and autumn, whereas ApERF4 functions as a repressor, suppressing pigment synthesis in summer. This antagonistic regulatory switch explains how plants dynamically reprogram leaf color in response to seasonal progression.
“Seasonal leaf coloration is a complex trait that cannot be explained by single genes alone,” said the corresponding author of the study. “By combining multiple layers of molecular data, we were able to see how transcription factors, chromatin structure, and DNA methylation work together as an integrated system. The discovery of a reversible regulatory module that switches pigment production on and off across seasons provides a new perspective on how plants fine-tune visible traits in response to environmental rhythms.”
Beyond explaining a familiar natural phenomenon, these findings have practical implications for ornamental plant breeding and landscape horticulture. Understanding the regulatory logic behind seasonal pigmentation opens new opportunities to precisely manipulate leaf color duration and intensity through molecular breeding or epigenetic approaches. The regulatory module identified in this study may also serve as a model for exploring seasonal trait plasticity in other plant species. More broadly, the work highlights how multi-omics integration can reveal hidden layers of gene regulation, offering powerful tools for decoding complex traits shaped by both genetics and the environment.
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References
DOI
10.1093/hr/uhaf257
Original Source URL
https://doi.org/10.1093/hr/uhaf257
Funding information
This research was supported by the National Natural Science Foundation of China (Project No. 32301660 and 32271914).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.