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Agronomy
Special Issues
Application of Multi-Omics and Systems Biology in Crop Breeding
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Application of Multi-Omics and Systems Biology in Crop Breeding

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 25 May 2025 | Viewed by 1278

Special Issue Editor

Dr. Wei Zhang

E-Mail Website
Guest Editor
Institute for Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
Interests: genomics and epigenomics; systems biology; network biology; modeling omics data; plant breeding and biotechnology; plant-microbe interaction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The application of multi-omics and systems biology in crop breeding represents a transformative paradigm shift in modern agriculture, aiming at enhancing crop improvement strategies. By integrating various omics technologies such as phenomics, genomics, transcriptomics, epigenomics, proteomics, and metabolomics, researchers gain a comprehensive understanding of the molecular mechanisms underlying complex traits in plants. The synergy between multi-omics and systems biology holds immense potential for revolutionizing plant breeding practices and addressing global challenges in food security and sustainability. However, integrating multiple omics platforms remains a challenge for many researchers due to inherent data differences.

This Special Issue seeks to cover a wide range of topics, including phenomics, genomics, transcriptomics, epigenomics, proteomics, metabolomics, and computational modeling, with the goal of enhancing crop productivity, stress tolerance, and nutritional quality. We welcome original research articles and reviews that showcase innovative applications of multi-omics and systems biology in crop breeding.

Dr. Wei Zhang
Guest Editor

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 100 words) can be sent to the Editorial Office for announcement on this website.

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. Agronomy 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 2600 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

  • multi-omics
  • phenomics
  • genomics
  • epigenomics
  • transcriptomics
  • proteomics
  • metabolomics
  • systems biology
  • crop breeding
  • plant–microbe interaction

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Published Papers (2 papers)

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Research

26 pages, 5531 KiB  
Article
Integration of Transcriptomics and Metabolomics Provides Insight into the Growth-Promoting Functions of Solanum khasianum Endophyte in Medicago sativa
by Jiahui Li, Shijia Zhou, Jiaru Fang, Qihang Cai, Yanbo Yang, Zhenghai Sun, Liping Li and Weiwei Li
Agronomy 2025, 15(1), 251; https://doi.org/10.3390/agronomy15010251 - 20 Jan 2025
Viewed by 372
Abstract
Medicago sativa is an important forage crop; its value is mainly concentrated in its economic aspects. The growth cycle and growth rate of M. sativa have an important influence on its economic benefits. Alternaria alstroemeriae has often been used as a pathogenic bacterium [...] Read more.
Medicago sativa is an important forage crop; its value is mainly concentrated in its economic aspects. The growth cycle and growth rate of M. sativa have an important influence on its economic benefits. Alternaria alstroemeriae has often been used as a pathogenic bacterium in previous studies, and studies on the growth-promoting effects of A. alstroemeriae are rare. This study aimed to assess the effects of A. alstroemeriae on the growth parameters of M. sativae and to investigate the molecular and metabolic mechanisms of M. sativa. M. sativa showed significant improvement in plant height, root length, fresh weight, and dry weight compared to uninoculated control plants. By integrating the results of transcriptome and metabolome analysis, A. alstroemeriae may promote plant growth by regulating genes associated with the biosynthetic pathways of flavonoids, anthocyanins, and proanthocyanidins in plants. These research findings provide a theoretical basis for future verification of the molecular response mechanisms and metabolic regulation of A. alstroemeriae-promoted plant growth. This study also provides a theoretical basis for sustainable agricultural development. Full article
(This article belongs to the Special Issue Application of Multi-Omics and Systems Biology in Crop Breeding)
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43 pages, 28157 KiB  
Article
Exploring the Physiological and Molecular Mechanisms by Which Potassium Regulates Low-Temperature Tolerance of Coconut (Cocos nucifera L.) Seedlings
by Lilan Lu, Yuping Wang, Md. Abu Sayed, Amjad Iqbal and Yaodong Yang
Agronomy 2024, 14(12), 2983; https://doi.org/10.3390/agronomy14122983 - 14 Dec 2024
Viewed by 635
Abstract
Coconut holds significant importance as a fruit and oilseed crop in tropical and subtropical regions. However, low-temperature (LT) stress has caused substantial reductions in yield and economics and impedes coconut production, therefore constraining its widespread cultivation and utilization. The appropriate application of potassium [...] Read more.
Coconut holds significant importance as a fruit and oilseed crop in tropical and subtropical regions. However, low-temperature (LT) stress has caused substantial reductions in yield and economics and impedes coconut production, therefore constraining its widespread cultivation and utilization. The appropriate application of potassium (K) has the potential to enhance the cold tolerance of crops and mitigate cold damage, but the regulatory mechanisms by which K improves coconut adaptability to cold stress remain poorly understood. Transcriptome and metabolomic analyses were performed on coconut seedlings treated with LT (5 °C) and room temperature (25 °C) under various K conditions: K0 (0.1 mM KCL), KL (2 mM KCL), KM (4 mM KCL), and KH (8 mM KCL). Correlation analysis with physiological indicators was also conducted. The findings indicated that K absorption, nutrient or osmotic regulation, accumulation of substances, photosynthesis, hormone metabolism, and reactive oxygen species (ROS) clearance pathways played crucial roles in the adaptation of coconut seedlings to LT stress. LT stress disrupted the homeostasis of hormones, antioxidant enzyme activity, chlorophyll, K, and the regulation of nutrients and osmolytes. This stress also leads to the downregulation of genes and metabolites related to K transporters, hormone metabolism, transcription factors, and the metabolism of nutrients and osmolytes. Applying K helped maintain the homeostasis of hormones, antioxidant enzyme activity, chlorophyll, K, and the regulation of nutrients and osmolytes, promoted the removal of ROS, and reduced malondialdehyde, consequently diminishing the damage caused by LT stress to coconut seedlings. Furthermore, the comprehensive analysis of metabolomics and transcriptomics highlighted the importance of carbohydrate metabolism, biosynthesis of other secondary metabolites, amino acid metabolism, lipid metabolism, and ABC transporters in K’s role in improving coconut seedlings’ tolerance to LT stress. This study identified the pivotal biological pathways, regulatory genes, and metabolites implicated in K regulation of coconut seedlings to acclimate to LT stress. Full article
(This article belongs to the Special Issue Application of Multi-Omics and Systems Biology in Crop Breeding)
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