Plant Metabolome and Metabolomics

A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: 31 January 2026 | Viewed by 645

Special Issue Editor


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Guest Editor
Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
Interests: plant physiology; plant biochemistry; plant growth and development; plant molecular biology; plant biotechnology and metabolic engineering; carbon and nitrogen metabolism; metabolome and transcriptome analyses
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Special Issue Information

Dear Colleagues,

Studies of the plant metabolome and metabolomics tools provide powerful opportunities for understanding plant responses to environmental and genetic factors, with significant applications in biotechnology, crop improvement, and sustainable agriculture as well as the production of unique drugs for human health. This Special Issue will highlight cutting-edge research using metabolomics to explore metabolic pathways, plant adaptation mechanisms, and innovative bi-technological approaches. We aim to bring together studies focusing on new and unique metabolites and modern techniques to analyze their structure and function in the life of plants, including current advances in their mass production for biomedical purposes. Genetic manipulation of their biosynthesis in plants is an integral component of these processes. The scope includes high-throughput metabolomics techniques for analyses and advances in data processing and bioinformatics. This issue will also explore plant metabolic pathways and their regulation, including both primary and secondary metabolites in plants, metabolic regulation under environmental stress such as drought, temperature, and salinity, and metabolite-mediated plant interactions with pathogens and insects. We encourage contributions that explore quantitative approaches, novel data integration strategies, and their applications in understanding plant responses to environmental and genetic factors.

Prof. Dr. Subhash Minocha
Guest Editors

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Keywords

  • metabolomics
  • LC/MS-based metabolomics
  • plant science
  • metabolic pathways
  • biotechnology applications
  • sustainable agriculture

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Published Papers (1 paper)

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Research

16 pages, 7346 KB  
Article
Multi-Omics Insights into Altered Flavonoid Metabolism Underlying Skin Color Variation in a Bud Mutant of Vitis vinifera Zaoheibao
by Liping Huang, Xi Dai, Linan Zhang, Yue Zhu, Min Wang, Zhili Xun, Qifeng Zhao and Jiancheng Zhang
Metabolites 2025, 15(10), 675; https://doi.org/10.3390/metabo15100675 - 16 Oct 2025
Viewed by 377
Abstract
Background: Fruit skin color is a key determinant of grape quality and market value, primarily governed by anthocyanin biosynthesis. Methods: In this study, we explored the molecular basis of skin color variation in the grape cultivar Zaoheibao and its bud mutant, which displays [...] Read more.
Background: Fruit skin color is a key determinant of grape quality and market value, primarily governed by anthocyanin biosynthesis. Methods: In this study, we explored the molecular basis of skin color variation in the grape cultivar Zaoheibao and its bud mutant, which displays a striking shift from purple-black to yellow-green. Integrated metabolomic and transcriptomic analyses revealed extensive reprogramming of the flavonoid pathway in the mutant. Results: Metabolite profiling identified 233 differentially accumulated metabolites (DAMs), with a drastic reduction in anthocyanins, particularly cyanidin- and peonidin-derivatives, together with altered levels of flavonols and flavonoid glycosides. Transcriptome analysis detected 4036 differentially expressed genes (DEGs), with key anthocyanin biosynthetic genes (DFR, ANS, UFGT, GST) and MYB significantly downregulated. Multi-omics integration confirmed consistent enrichment of flavonoid-related pathways, while correlation network analysis highlighted strong associations between MYB regulators, structural genes, and anthocyanin-type metabolites. Conclusions: Collectively, these findings demonstrate that suppression of a MYB-centered regulatory module underlies the loss of pigmentation in the bud mutant, providing new insights into the molecular regulation of grape skin coloration and a theoretical basis for grape breeding and quality improvement. Full article
(This article belongs to the Special Issue Plant Metabolome and Metabolomics)
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