For centuries, the concept of “geoherbalism” has underscored that traditional Chinese medicines grown in specific regions produce superior therapeutic effects. Temperature is a critical factor shaping the chemistry of these herbs, but climate change threatens to disrupt this balance. Previous studies in crops and model plants have shown that epigenetic modifications, such as DNA methylation and histone marks, influence how plants respond to environmental stress. However, in medicinal herbs, the mechanisms connecting warming with metabolite production remain largely unexplored. Due to these challenges, it is necessary to conduct in-depth research on the epigenetic basis of herb adaptation to climate stress.
Researchers from China Three Gorges University and collaborators published (DOI: 10.1093/hr/uhae328) their findings on March 1, 2025, in Horticulture Research. Using advanced sequencing technologies, the team assembled a chromosome-scale genome of Scrophularia ningpoensis and performed epigenomic and metabolic profiling across tissues. Their study reveals that histone methylation patterns shift with temperature, regulating the synthesis of iridoids, the plant’s key therapeutic compounds. The work offers a genomic and epigenomic foundation for understanding how medicinal plants respond to warming, with implications for preserving herb quality under global climate change.
The team produced a high-quality, haplotype-resolved genome of S. ningpoensis totaling 730 Mb, anchoring sequences to 92 pseudochromosomes. Comparative analysis identified more than 89,000 protein-coding genes and thousands of non-coding RNAs, confirming the plant’s complex genomic architecture. Epigenomic profiling revealed distinct histone modifications: H3K27ac and H3K4me3 were associated with active transcription, while H3K36me3 emerged as a key regulatory mark in roots, where most iridoids accumulate. Temperature simulation experiments showed that moderate warming enhanced iridoid synthesis, whereas excessive heat reduced survival. Crucially, the histone methyltransferase gene SnSDG8 was identified as a regulator of H3K36me3 deposition in iridoid biosynthesis genes. Functional validation in tobacco leaves confirmed that overexpressing SnSDG8 increased H3K36me3 levels and activated iridoid pathway genes, including SnAACT. These results demonstrate a molecular link between warming, histone methylation, and metabolite production. The findings provide a multi-omics perspective on how environmental cues shape the chemistry and therapeutic potential of traditional herbal medicines.
“Our study sheds light on how subtle shifts in climate can reprogram the medicinal value of herbs at the molecular level,” said lead author Chao Zhou. “By revealing that SnSDG8-mediated histone methylation directly regulates iridoid biosynthesis, we now understand why Scrophularia ningpoensis thrives under moderate warmth and how its bioactive compounds are maintained. These insights not only advance the biology of geoherbalism but also provide practical guidance for medicinal plant breeding. Protecting herb quality under global warming requires integrating genomics and epigenetics into cultivation strategies.”
This work provides the first chromosome-scale reference genome and epigenetic atlas for S. ningpoensis, establishing a foundation for precision breeding of climate-resilient medicinal plants. By linking H3K36me3 dynamics with iridoid biosynthesis, the study offers biomarkers for monitoring plant responses to temperature fluctuations. The discovery also supports adaptive agricultural practices, such as relocating cultivation zones to optimal temperature regions. More broadly, it highlights the role of epigenetics in safeguarding the consistency and quality of traditional medicines as global temperatures rise. These insights will be vital for ensuring reliable herbal resources in the face of ongoing environmental change.
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References
DOI
10.1093/hr/uhae328
Original Source URL
https://doi.org/10.1093/hr/uhae328
Funding information
The financial assistance for this research was provided by the grants from the Open Project of Hubei Key Laboratory of Wudang Local Chinese Medicine Research (WDCM2023014) to C.Z. and Principal Investigator Program (HBMUPI202104) to Y. Z. at Hubei University of Medicine, and Open Foundation of Hubei Province Key Laboratory of Tumor Microenvironment and Immunotherapy (2023KZL026) to Q.X.
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.