Spuriopimpinella brachycarpa, known locally as Dayeqin or Shanqincai, has long been used in traditional medicine to treat colds, indigestion, abdominal pain, and cough. Modern pharmacology has confirmed its extracts possess multiple bioactivities, including hepatoprotective, lipid-regulating, anti-neuroinflammatory, and antioxidant effects. Flavonoids and terpenoids are particularly abundant in this species and contribute to its antimicrobial and anti-proliferative properties. Yet despite its evident value, genetic studies on this plant have remained preliminary, and the regulatory mechanisms underlying its key bioactive compounds have been largely unexplored. Genomic resources for aromatic Apiaceae species with medicinal and edible potential remain scarce. Based on these challenges, an in-depth investigation into the biosynthesis pathways and environmental regulation of flavonoids and terpenoids in S. brachycarpa is urgently needed.
A team of researchers from Jilin Agricultural University, Northeast Normal University, Nanjing Agricultural University, and the University of British Columbia has published (DOI: 10.1093/hr/uhag107) the first chromosome-level genome assembly of Spuriopimpinella brachycarpa in Horticulture Research (2026, Vol. 13, Issue 7). The 4.12-Gb genome, organized into 11 chromosomes, enabled a systematic multiomics analysis that identified key genes and regulatory networks controlling flavonoid and terpenoid biosynthesis, revealing how different habitats—wild forest, forest-simulated, and cultivated open fields—shape the accumulation of these valuable metabolites.
The genome assembly, with a scaffold N50 of 358.95 Mb and 95% BUSCO completeness, revealed that S. brachycarpa experienced two whole-genome duplication (WGD) events—one ancestral shared across the Apiaceae family and a more recent lineage-specific duplication. These genetic doublings likely provided the raw material for the evolution of secondary metabolism and environmental adaptation. Metabolomic profiling identified 1,623 metabolites, with flavonoids—dominated by flavanols and flavones—most actively synthesized in leaves. Terpenoids, primarily monoterpenes and sesquiterpenes, showed a striking habitat-dependent pattern: they accumulated predominantly under open cultivated conditions, suggesting that greater sunlight exposure and abiotic stress promote their production.
The study pinpointed a candidate MYB (myeloblastosis) transcription factor, SbraChr11G00348720.1, as a likely master regulator of flavonoid biosynthesis, showing co-expression links with key structural genes including SbDFR, SbC4H, and SbFLS. For terpenoids, two terpene synthase (TPS) genes emerged as core candidates—SbraChr6G00204720.1 (TPS-a subfamily) associated with sesquiterpene biosynthesis and SbraChr3G00078100.1 (TPS-b subfamily) linked to monoterpene production. The TPS-a subfamily dominated with 29 members, while TPS-b contributed 20, together accounting for over 90% of the 54 TPS genes identified—a repertoire expanded compared to related species, possibly reflecting adaptation to the Changbai Mountain climate.
"The genome gives us a window into how this plant produces its most valuable compounds," the authors said. "We were particularly struck by how dramatically the growing environment shapes terpenoid accumulation—plants in open fields produced far more of these defense-related metabolites than their wild counterparts. The MYB transcription factor we identified appears to be a key switch controlling flavonoid production in leaves, which makes sense given that leaves are the primary site of photosynthesis and need protection from oxidative stress. These findings give us concrete targets for breeding and cultivation strategies to enhance the medicinal quality of this plant."
The findings have immediate practical implications for sustainable cultivation and quality improvement of S. brachycarpa. With wild populations severely depleted by overharvesting, cultivation has become essential for large-scale production. Understanding how environmental factors—particularly light exposure—drive terpenoid accumulation provides a scientific basis for optimizing cultivation practices to enhance yields of these bioactive compounds. The identified MYB transcription factor and TPS genes offer promising targets for molecular breeding and metabolic engineering, potentially enabling the development of varieties with enhanced flavonoid or terpenoid content. Beyond this species, the high-quality genome serves as a valuable resource for comparative genomics across the Apiaceae family, supporting research on phylogenetic evolution and functional gene diversification in other medicinal and edible plants.
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References
DOI
10.1093/hr/uhag107
Original Source URL
https://doi.org/10.1093/hr/uhag107
Funding information
This research was funded by Jilin Agricultural University high-level researcher grant (JLAUHLRG20102006) and Jilin Provincial Department of Human Resources and Social Security (grant: no. 201020012). This study is also supported by the 111 Project, Northeast Advantageous Characteristic Resources and Health Food Discipline Innovation Introduction Base (grant no. D23007).
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.