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Horticulturae
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Breeding, Cultivation and Metabolic Regulation of Medicinal Plants—2nd Edition
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Breeding, Cultivation and Metabolic Regulation of Medicinal Plants—2nd Edition

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Medicinals, Herbs, and Specialty Crops".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 5965

Special Issue Editors

Prof. Dr. Mengfei Li

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Guest Editor
State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
Interests: variety breeding; ecological adaptability; metabolic regulation; multi-omics of medicinal plants
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jianhe Wei

E-Mail Website
Guest Editor
Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
Interests: cultivation, molecular breeding, and regulation of secondary metabolites of medicinal plants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Today, there are over 50,000 medicinal plants (syn. medicinal herbs) widely used for fighting diseases, relieving aches, and dispelling mosquitoes and other insects—along with other purposes—which largely rely on bioactive metabolites such as alkaloids, flavonoids, phenylpropanoids, etc. With increasing commercial demand all over the world, it is urgent and necessary to produce these high-quality medicinal plants through the selective breeding of good varietites, the optimization of cultivation modes (e.g., eco-planting, wild tending, and Bionic wild planting), and metabolic regulation by environmental factors (e.g., temperatures, light, and nutrition), while preventing and controlling diseases and pests. The aim of this Special Issue is to collect original research and review articles that address recent advances in the breeding, cultivation, and metabolic regulation of medicinal plants. Studies on cell and tissue culture, rapid propagation, and water planting will also be considered.

Prof. Dr. Mengfei Li
Prof. Dr. Jianhe Wei
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Horticulturae is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • medicinal plants
  • variety breeding
  • cultivation mode
  • metabolic regulation
  • multi-omics

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Related Special Issue

Published Papers (6 papers)

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Research

18 pages, 5835 KB  
Article
Transcriptome-Based Discovery of Tuber Formation Genes in Asparagus cochinchinensis and A. taliensis Provides Targets for Breeding Improvement
by Dan Liu, Aimeng Chen, Feili Yan, Xiongwei Liu, Jiahui Wu, Siqi Liu, Xue Wu, Siyu Liang, Jun Zhao, Ma Yu and Xiangyang Lyu
Horticulturae 2026, 12(2), 202; https://doi.org/10.3390/horticulturae12020202 - 5 Feb 2026
Viewed by 404
Abstract
The genus Asparagus L. is a traditional Chinese herb valued for its medicinal and culinary properties, with root tubers being the primary organ of interest. To elucidate the genetic mechanisms underlying tuber formation, we conducted a comparative transcriptome analysis of two species, Asparagus [...] Read more.
The genus Asparagus L. is a traditional Chinese herb valued for its medicinal and culinary properties, with root tubers being the primary organ of interest. To elucidate the genetic mechanisms underlying tuber formation, we conducted a comparative transcriptome analysis of two species, Asparagus cochinchinensis (Lour.) Merr. and Asparagus taliensis F. T. Wang & Tang ex S. C. Chen, which exhibit distinct differences in root tuber number. High-throughput sequencing generated 6.68 Gb and 7.60 Gb of clean data for the respective species, leading to the annotation of 115,080 non-redundant unigenes. Comparative analysis identified 26,013 differentially expressed genes (DEGs), including 1096 associated with carbohydrate metabolism. Weighted gene co-expression network analysis (WGCNA) revealed that the MEred and Megreenyellow modules which included genes involved in material and energy metabolism were significantly correlated with tuber development. From these modules, we identified two candidate genes involved in carbon and sugar metabolism, designated Ac_uniYEAD and Ac_uniRPE. Quantitative real-time PCR validation confirmed that their expression levels were positively correlated with root tuber number, consistent with the transcriptomic data. These results highlight Ac_uniYEAD and Ac_uniRPE as promising targets for genetic improvement of tuber yield in Asparagus breeding programs. Full article
(This article belongs to the Special Issue Breeding, Cultivation and Metabolic Regulation of Medicinal Plants—2nd Edition)
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19 pages, 5231 KB  
Article
Symbiotic Cultivation of Gastrodia elata: Armillaria Strain Selection Reprograms Carbon Allocation to Balance Tuber Yield and Phenolic Glycosides
by Zhilong Shi, Zhonglian Ma, Yong Wang, Li Dong, Yafei Guo, Liping Xu and Shunqiang Yang
Horticulturae 2026, 12(2), 181; https://doi.org/10.3390/horticulturae12020181 - 31 Jan 2026
Cited by 1 | Viewed by 770
Abstract
Gastrodia elata is a fully mycoheterotrophic orchid whose tuber development depends on carbon delivered by Armillaria fungi. Its formal inclusion in China’s “medicine and food homology” catalog has intensified demand for cultivated tubers combining high yield with consistent bioactive quality. Here, we tested [...] Read more.
Gastrodia elata is a fully mycoheterotrophic orchid whose tuber development depends on carbon delivered by Armillaria fungi. Its formal inclusion in China’s “medicine and food homology” catalog has intensified demand for cultivated tubers combining high yield with consistent bioactive quality. Here, we tested whether Armillaria mellea strains steer host carbon allocation between biomass accumulation and phenolic glycoside biosynthesis. Using a standardized EPS symbiotic cultivation system (AM1, AM2, AM3; n = 3 biological replicates per strain), we integrated agronomic traits with widely targeted metabolomics and RNA-seq transcriptomics, including weighted gene co-expression network analysis (WGCNA). AM3 produced the highest tuber yield and higher primary carbon status (PCAI), but lower gastrodin/parishin-type phenolic glycosides and lower allocation efficiency (BER), whereas AM1 showed a quality-dominant profile with significantly higher BER. WGCNA highlighted an AM3-associated module enriched in starch-biosynthetic genes, and PCAI was strongly negatively correlated with the weighted Parishin-Gastrodin Index (wPGI) across samples (n = 9), consistent with a carbohydrate-storage versus phenolic-glycoside trade-off. These results indicate that fungal strain identity functions as an external regulator of source–sink dynamics in G. elata, supporting “precision symbiosis” for food-grade versus medicinal-grade production. Full article
(This article belongs to the Special Issue Breeding, Cultivation and Metabolic Regulation of Medicinal Plants—2nd Edition)
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17 pages, 1954 KB  
Article
Variation in the Number of Genes in the Secretomes of Isolates of Ilyonectria robusta and Ilyonectria mors-panacis Pathogenic to American Ginseng (Panax quinquefolius)
by Paul H. Goodwin, Moez Valliani and Tom Hsiang
Horticulturae 2026, 12(2), 135; https://doi.org/10.3390/horticulturae12020135 - 25 Jan 2026
Viewed by 511
Abstract
For 12 isolates of Ilyonectria mors-panacis and 4 isolates of Ilyonectria robusta, the number of genes in the secretome showed a negative correlation with growth rates in culture, especially for small secreted non-cysteine-rich and cysteine-rich proteins, and several proteases and lipases, while it [...] Read more.
For 12 isolates of Ilyonectria mors-panacis and 4 isolates of Ilyonectria robusta, the number of genes in the secretome showed a negative correlation with growth rates in culture, especially for small secreted non-cysteine-rich and cysteine-rich proteins, and several proteases and lipases, while it was positively correlated with genes for six CAZyme classes/modules and other proteases and lipases. However, this significant correlation with growth rate was influenced by the I. robusta isolates mostly having faster growth rates than the I. mors-panacis isolates on PDA, indicating a species-level difference. The only significant relationship of gene number to virulence was a positive correlation with genes for secreted glycoside hydrolases in families 18 and 78, and this was related to differences between isolates, even if only I. mors-panacis isolates were examined, indicating a difference within species. Glycoside hydrolase family 18 includes chitinase-like proteins, endo-β-N-acetylglucosaminidases, lectins, and xylanase inhibitors, which could help suppress triggered immunity by the host and regulate fungal xylanase activity. Glycoside hydrolase family 78 contain α-L-rhamnosidases that can cleave flavonoid glycosides, saponins, and ginsenosides, which could degrade antimicrobial compounds produced as a host response during infection. These results indicate that the number of certain classes of secreted enzymes could be a factor in both growth rate in culture and virulence. Full article
(This article belongs to the Special Issue Breeding, Cultivation and Metabolic Regulation of Medicinal Plants—2nd Edition)
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22 pages, 67029 KB  
Article
An Integrated Analysis of WRKY Genes in Autotetraploid Bupleurum chinense: Evolution, Stress Response, and Impact on Saikosaponin Biosynthesis
by Chuanxin Mo, Wenshuai Chen, Zhen Wei, Yuchan Li, Xueling Wang, Mingyue Yan, Jun Zhao, Zeru Yu, Chao Xin, Ma Yu and Hua Chen
Horticulturae 2026, 12(1), 102; https://doi.org/10.3390/horticulturae12010102 - 18 Jan 2026
Viewed by 553
Abstract
WRKY transcription factors play critical roles in plant growth, development, metabolism, and stress responses. In this study, we performed the first genome-wide characterization of the WRKY gene family in Bupleurum chinense, using a T2T-level assembly of the autotetraploid genome. A total of [...] Read more.
WRKY transcription factors play critical roles in plant growth, development, metabolism, and stress responses. In this study, we performed the first genome-wide characterization of the WRKY gene family in Bupleurum chinense, using a T2T-level assembly of the autotetraploid genome. A total of 303 BcWRKY genes were identified and found to be unevenly distributed across four subgenomes. Phylogenetic and structural analyses revealed that segmental duplications after polyploidization drove lineage-specific expansion of the family. Meta-transcriptome analysis demonstrated that BcWRKY genes exhibited tissue-specific expression patterns and dynamic responses to stress, suggesting functional diversification. Under drought, waterlogging, methyl jasmonate, and ABA treatments, the contents of saikosaponins A and D significantly increased. This increase was accompanied by transcriptional activation of multiple BcWRKY genes. Correlation analysis between ten BcWRKYs and ten saikosaponins biosynthetic associated genes (BcBASs, BcCYPs, and BcUGTs) identified BcWRKY22, BcWRKY33, and BcWRKY46 as potential regulators of saikosaponin metabolism under stress conditions. Our study provided a comprehensive framework for understanding BcWRKY gene evolution and secondary metabolic regulation in polyploid medicinal plants. It also offered candidate genes for breeding B. chinense cultivars with high saikosaponin content. Full article
(This article belongs to the Special Issue Breeding, Cultivation and Metabolic Regulation of Medicinal Plants—2nd Edition)
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14 pages, 3014 KB  
Article
Responses of Growth and Secondary Metabolites in Fish Mint (Houttuynia cordata Thunb.) Cuttings to Far-Red Light
by Zi-Yi Wang, Kuan-Hung Lin, Yen-Chi Yin and Chang-Chang Chen
Horticulturae 2025, 11(10), 1237; https://doi.org/10.3390/horticulturae11101237 - 13 Oct 2025
Viewed by 1809
Abstract
Fish mint (Houttuynia cordata Thunb.) is an aromatic herb used as food and medicine across Asia. We evaluated how far-red (FR) light influences growth and secondary metabolites in the non-flowering cultivar ‘BCV02’ propagated by cuttings. Seedlings were grown for 14 days under [...] Read more.
Fish mint (Houttuynia cordata Thunb.) is an aromatic herb used as food and medicine across Asia. We evaluated how far-red (FR) light influences growth and secondary metabolites in the non-flowering cultivar ‘BCV02’ propagated by cuttings. Seedlings were grown for 14 days under FR at 35, 50, and 70 μmol m−2 s−1 (as FR35, 50, and 70, respectively) or without FR (as control, CK). All FR treatments increased plant height but reduced the shoot/rhizome ratio. Total chlorophyll and carotenoid contents were unchanged, while the chlorophyll a/b ratio declined from 2.37 (CK) to 2.15 (FR70). In shoots, combined 3-, 4-, and 5-O-caffeoylquinic acids with rutin, hyperoside, isoquercitrin, and quercitrin reached 12.61–13.83 mg g−1 dry weight (DW) under FR treatments, exceeding CK (8.48 mg g−1 DW). However, in rhizomes, these secondary metabolite contents ranged 0.82–1.00 mg g−1 DW across all treatments. On a per-pot basis, the highest accumulated compounds (4.37 mg per pot) occurred at FR35. Overall, growth and secondary metabolite biosynthesis in fish mint cuttings respond differently to changes in FR treatments, with FR35 optimizing compound accumulation. Quercitrin in shoots was 0.09–0.20 mg g−1 DW and not quantifiable in rhizomes, potentially below pharmacopeial thresholds specified in the Taiwan Herbal Pharmacopeia and Hong Kong Chinese Materia Medica Standards. These results underscore the importance of aligning cultivar choice, light regime, and market specifications to secure both yield and quality of H. cordata. Full article
(This article belongs to the Special Issue Breeding, Cultivation and Metabolic Regulation of Medicinal Plants—2nd Edition)
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19 pages, 5645 KB  
Article
Characterization of Complete Chloroplast Genome Sequences of Three Tropical Liana Dalbergia Species and Comparative Analysis of Phylogenetic and Structure Variations in Dalbergia Genus
by Jun Wang, Shaoying Zheng, Xianglai Sun, Lulu Wang and Xupo Ding
Horticulturae 2025, 11(7), 799; https://doi.org/10.3390/horticulturae11070799 - 5 Jul 2025
Viewed by 1350
Abstract
The Dalbergia genus, a morphologically diverse group within the Fabaceae family, encompasses species of significant value in furniture production and medicinal and aromatic applications. The taxonomy of Dalbergia has relied on morphological traits, chloroplast (cp) DNA fragments, and cp genomic data. However, genomic [...] Read more.
The Dalbergia genus, a morphologically diverse group within the Fabaceae family, encompasses species of significant value in furniture production and medicinal and aromatic applications. The taxonomy of Dalbergia has relied on morphological traits, chloroplast (cp) DNA fragments, and cp genomic data. However, genomic resources for tropical liana species within this genus remain scarce. In this study, we assembled and analyzed the cp genomes of 3 liana species—Dalbergia peishaensis, D. pinnata, and D. tsoi—and compared them with those of 26 other Dalbergia species to explore their cp genome characteristics and evolutionary patterns. We employed a combination of traditional cp genome analysis and methods adapted from plant whole-genome sequencing. Phylogenetic analysis revealed that D. peishaensis has a close relationship with D. cultrata, forming a recently diverged clade, whereas D. tsoi and D. pinnata are positioned within a basal clade of the Dalbergia genus, suggesting an earlier divergence. The Dalbergia cp genomes exhibit considerable variation in size, with evidence of pseudogenization, gene loss, and duplication observed in the three liana species. Notably, the infA gene, previously reported as absent in the chloroplast genomes of Dalbergia species, was identified in the cp genomes of these three liana Dalbergia species. A total of 4533 simple sequence repeats (SSRs) were identified, providing valuable insights into cp genome evolution and facilitating future population genetics studies, particularly when combined with the high structural variation observed in the genus through whole-genome analysis methods. Additionally, seven highly divergent regions were identified as potential DNA barcode hotspots. This study enhances the genomic characterization of liana Dalbergia species and offers a robust framework for future plant cp genome analyses by integrating methodologies originally developed for whole-genome studies. Full article
(This article belongs to the Special Issue Breeding, Cultivation and Metabolic Regulation of Medicinal Plants—2nd Edition)
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