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Horticulturae
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Genes and Their Regulatory Networks Underlying Secondary Metabolite Biosynthesis in...
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Genes and Their Regulatory Networks Underlying Secondary Metabolite Biosynthesis in Horticultural Crops

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 2870

Editors

Dr. Yue Yin

E-Mail
Guest Editor
National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 751002, China
Interests: molecular breeding; DNA methylation; gene mining of quality traits; gene editing; transcriptional regulation of secondary metabolites
Dr. Lingxia Wang

E-Mail Website
Guest Editor
School of Life Sciences, Ningxia University, Yinchuan 750021, China
Interests: salt stress; plant physiology; protein modification; gene function

Special Issue Information

Dear Colleagues,

The fruits of horticultural plants are rich in secondary metabolites such as flavonoids, terpenoids, and alkaloids. Their content and composition are important quality indicators for evaluating fruit quality, and they also play a significant role in human health and response to adverse stress.

A large number of horticultural plants have completed whole-genome sequencing to identify the members of gene families that regulate important secondary metabolites, providing excellent gene resources for revealing the diversity of secondary metabolism formation and targeted breeding of varieties.

It is necessary to identify the members of the gene family that regulate the secondary metabolites of horticultural plants at the whole-genome level and obtain candidate genes through the correlation analysis of gene expression and secondary metabolites.

This Special Issue welcomes research on the identification and expression of related gene families in important secondary metabolites of horticultural plants, including the identification of gene family members, evolution and replication events, and studies related to the content of secondary metabolites and gene expression.

Dr. Yue Yin
Dr. Lingxia Wang
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-anonymized 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 2400 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

  • horticultural crops
  • secondary metabolites
  • secondary metabolite biosynthesis pathway
  • biosynthesis mechanisms
  • transcription factors
  • regulatory networks
  • transcriptional regulation
  • epigenetic regulation
  • post-transcriptional regulation

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Published Papers (3 papers)

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Research

17 pages, 2452 KB  
Article
Overexpression of the Lavender LaDXS2-2 Gene in Tobacco Modulates the MEP Pathway to Improve Photosynthetic Efficiency and Alter Primary Metabolism: Evidence from Integrated Omics Analyses
by Xinyue Tang, Mingyang Sun, Qichen He, Liping Yang, Lingna Chen and Yongkun Chen
Horticulturae 2026, 12(6), 753; https://doi.org/10.3390/horticulturae12060753 - 20 Jun 2026
Viewed by 639
Abstract
1-Deoxy-D-xylulose-5-phosphate synthase (DXS) serves as the initial rate-limiting enzyme in the methylerythritol phosphate (MEP) pathway, governing the biosynthesis of precursors for photosynthetic pigments and terpenoids. In this study, the LaDXS2-2 gene was cloned and functionally characterized in lavender (Lavandula angustifolia). The [...] Read more.
1-Deoxy-D-xylulose-5-phosphate synthase (DXS) serves as the initial rate-limiting enzyme in the methylerythritol phosphate (MEP) pathway, governing the biosynthesis of precursors for photosynthetic pigments and terpenoids. In this study, the LaDXS2-2 gene was cloned and functionally characterized in lavender (Lavandula angustifolia). The full-length coding sequence (CDS) of LaDXS2-2 spans 2178 base pairs, encoding a protein of 725 amino acids. Phylogenetic analysis revealed that LaDXS2-2 is most closely related to the DXS from Salvia miltiorrhiza. Expression profiling demonstrated that LaDXS2-2 was highly expressed in flower buds, and its transcript levels were significantly upregulated (p < 0.05) in response to ethephon, high light intensity, and low temperature, while exhibiting tissue-specific responses to gibberellin application. Subcellular localization assays confirmed LaDXS2-2 is targeted to the chloroplast. Heterologous overexpression of LaDXS2-2 in tobacco resulted in a marked increase in photosynthetic pigment content, enhanced the actual photochemical efficiency of photosystem II [Y(II)], and reduced non-photochemical quenching (NPQ). Integrated transcriptomic and metabolomic analyses further revealed that LaDXS2-2 overexpression activated the diterpenoid biosynthesis pathway and upregulated amino acid metabolism as well as the TCA cycle, while competitively suppressing phenylpropanoid and flavonoid biosynthesis pathways. These findings indicate that LaDXS2-2 not only enhances photosynthetic efficiency by promoting the synthesis of photosynthetic pigments but also suggests a potential role in influencing primary carbon and nitrogen metabolism, as inferred from transcriptomic and metabolomic data. This functionality may ultimately influence plant growth and metabolic homeostasis. Overall, this study provides a theoretical foundation for the synergistic improvement of photosynthetic efficiency and secondary metabolism in crops. Full article
(This article belongs to the Special Issue Genes and Their Regulatory Networks Underlying Secondary Metabolite Biosynthesis in Horticultural Crops)
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19 pages, 19917 KB  
Article
Genome-Wide Identification of NAC Gene Family and Their Correlation Analysis with Sugar Metabolism in Wolfberry (Lycium barbarum L.)
by Yue Yin, Ji Mi, Bowei Yao, Jun He, Xiaorong Bai, Dekai Zhang, Wei An and Xiyan Zhang
Horticulturae 2026, 12(6), 705; https://doi.org/10.3390/horticulturae12060705 - 7 Jun 2026
Viewed by 854
Abstract
The NAM, ATAF, and CUC (NAC) transcription factors represent a major class of plant-specific transcription factors that regulate plant growth, development, and responses to various biotic and abiotic stresses. Despite their importance, limited information exists about this gene family in wolfberry (Lycium [...] Read more.
The NAM, ATAF, and CUC (NAC) transcription factors represent a major class of plant-specific transcription factors that regulate plant growth, development, and responses to various biotic and abiotic stresses. Despite their importance, limited information exists about this gene family in wolfberry (Lycium barbarum), a valuable traditional Chinese medicinal plant widely cultivated in northwest China. In this study, 107 LbaNAC genes were identified from the wolfberry genome and found to be unevenly distributed across 12 chromosomes. These LbaNAC genes were clustered into 18 subfamilies, with motif composition and gene structure showing high consistency with their phylogenetic relationships. A total of 192 orthologous gene pairs were identified between wolfberry and tomato, potato, Arabidopsis thaliana, and rice, respectively. Gene duplication analysis revealed that dispersed duplication was a major driver in the expansion of the LbaNAC gene family, while the analysis of the nonsynonymous (Ka) to synonymous (Ks) substitution rates confirmed that purifying selection has been the predominant evolutionary force acting on these genes. Cis-acting element analysis showed that their promoters harbor elements associated with growth, metabolism, and various stress responses. Furthermore, correlation analysis demonstrated that the expression profiles of LbaNAC001, 027, 043, 051, 053, and 080 were significantly and positively correlated with the dynamic changes in glucose, fructose, and sucrose contents in wolfberry fruits. Furthermore, quantitative real-time PCR validation of the selected LbaNAC genes confirmed that their expression patterns were consistent with the transcriptome data. Subcellular localization and transcriptional activation analyses revealed that LbaNAC027 is a nucleus-localized transcriptional activator. This study identifies potential LbaNACs involved in wolfberry fruit sugar metabolism, providing a theoretical foundation for elucidating their regulatory mechanisms. Full article
(This article belongs to the Special Issue Genes and Their Regulatory Networks Underlying Secondary Metabolite Biosynthesis in Horticultural Crops)
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17 pages, 5350 KB  
Article
Dynamic Accumulation and Transcriptional Regulation of Alkylamides in Developing Zanthoxylum planispinum var. Dintanensis Fruits
by Hang Zhang, Ning Lv, Xinglin Wang, Huan Tian, Lunxian Liu, Tie Shen and Qingxiong Yang
Horticulturae 2026, 12(3), 386; https://doi.org/10.3390/horticulturae12030386 - 20 Mar 2026
Viewed by 954
Abstract
The accumulation dynamics and regulatory mechanisms of the alkylamides, the key pungent compounds in the fruits of Sichuan peppers, remain poorly understood. Using fruits of the Zanthoxylum planispinum var. dintanensis (Dintan) harvested at five key developmental stages, we comprehensively mapped the accumulation of [...] Read more.
The accumulation dynamics and regulatory mechanisms of the alkylamides, the key pungent compounds in the fruits of Sichuan peppers, remain poorly understood. Using fruits of the Zanthoxylum planispinum var. dintanensis (Dintan) harvested at five key developmental stages, we comprehensively mapped the accumulation of numbering compounds and their underlying molecular drivers by integrating HPLC-based metabolite profiling and de novo transcriptomics. Total alkylamide content increased during development, with hydroxyl-α-sanshool (HαSS) being predominant. The contributions of hydroxyl-β-sanshool (HβSS) and hydroxyl-ε-sanshool (HεSS) increased in later stages. Cluster and correlation analyses identified 51 candidate genes strongly correlated (|r| ≥ 0.6) with HαSS accumulation, predominantly enriched in fatty acid and branched-chain amino acid metabolism pathways. The expression patterns of five stearoyl-CoA desaturase (SCD) genes, one long-chain acyl-CoA synthetase (ACSL/fadD), and one S-(hydroxymethyl)glutathione dehydrogenase/alcohol dehydrogenase (frmA) gene closely mirrored HαSS accumulation. In contrast, 3-oxoacyl-[acyl-carrier-protein] synthase II (fabF) and one β-ketoacyl-CoA synthase (KCS) gene exhibited a negative correlation. Accordingly, a positive regulatory network was constructed for HαSS accumulation. These findings revealed key candidate targets for deciphering the molecular basis of its unique flavor and for breeding high-pungency cultivars. Full article
(This article belongs to the Special Issue Genes and Their Regulatory Networks Underlying Secondary Metabolite Biosynthesis in Horticultural Crops)
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