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Plant Tissue Culture: Genomics, Proteomics, Transcriptomics, and Metabolomics Approaches
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Plant Tissue Culture: Genomics, Proteomics, Transcriptomics, and Metabolomics Approaches

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 2421

Special Issue Editors

Dr. Víctor M. Loyola-Vargas

E-Mail Website
Guest Editor
Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán, Mérida, Yucatán 97205, CP, Mexico
Interests: study the processes that trigger somatic embryogenesis; particularly the role of growth regulators; tools such as transcriptomics; proteomics; CRISPR editing; metabolomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Neftalí Ochoa-Alejo

E-Mail Website
Guest Editor
Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico
Interests: Capsicum; chili pepper; tissue culture; biochemistry; molecular biology; secondary compounds; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since Dr. Gottlieb Haberlandt made several predictions about the development of in vitro-cultured cells in 1902, the study and use of plant tissue culture have evolved extraordinarily to become how important they are today, both for the study of basic aspects of plant cell biology and for the development of technologies that are now commercially available.

The study of biological phenomena involving plant cells has benefited from using omic tools. In this Special Issue, we wish to compile—in the form of reviews, technical notes, and original research work—the most advanced information on using these tools in the study and development of plant tissue culture. The use of transcriptomics in the study of somatic embryogenesis and cell differentiation, proteomics in germplasm conservation studies, and genomics in obtaining haploids and hybrids, as well as the use of metabolomics during the study of the production of secondary metabolites in suspension cultures, are examples of how new technologies are allowing leaps and bounds of progress in understanding these biological phenomena.

We invite our colleagues from the field of tissue culture who are using omic techniques to contribute to this Special Issue and create an invaluable source of information for the plant science community.  

Specific topics of interest of this Special Issue include the following but not limited:

  • The use of transcriptomics during the establishment of somatic embryogenesis.
  • The proteomic study of cell differentiation.
  • The metabolomic analysis of the production of secondary metabolites by plant tissue culture.
  • The study of gene expression during the establishment of in vitro plant tissue culture.
  • Genomic studies during the production of haploids.
  • The use of transcriptomics during the study of plant regeneration.
  • Stress alterations in cell differentiation and metabolome in plants.
  • Proteomic and transcriptomic analyses of callogenesis.
  • Transcriptome study of the auxin-inducing rooting of calluses.
  • Genomic analysis of lncRNA in embryogenic competence.
  • Metabolomic analysis of high-value metabolites from callus culture.
  • Study of the genes related to somatic embryogenesis.
  • Omic studies during the cryopreservation of germplasm.
  • Proteomic studies of the induction of somatic embryogenesis.
  • Genome-wide studies of the homeostasis of plant growth regulators in plant tissue culture.
  • Genomic study of the genetic stability of plants produced in temporary immersion bioreactors.

Dr. Víctor M. Loyola-Vargas
Prof. Dr. Neftalí Ochoa-Alejo
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 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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • plant cell tissue culture
  • genomics
  • transcriptomics
  • epigenomics
  • proteomics
  • metabolomic plant cell differentiation
  • somatic embryogenesis
  • plant growth regulators

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Published Papers (2 papers)

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27 pages, 15201 KiB  
Article
Transcriptional Dynamics Underlying Somatic Embryogenesis in Coffea canephora
by Marcos-David Couoh-Cauich, Hugo A. Méndez-Hernández, Rosa M. Galaz-Ávalos, Ana Odetth Quintana-Escobar, Enrique Ibarra-Laclette and Víctor M. Loyola-Vargas
Plants 2025, 14(7), 1108; https://doi.org/10.3390/plants14071108 - 2 Apr 2025
Viewed by 520
Abstract
In Coffea canephora, a direct somatic embryogenesis (SE) protocol has been established by pretreating plants with NAA and kinetin, followed by the induction of leaf explants in a liquid medium with BA. Through a transcriptomic analysis of 10 key moments of the [...] Read more.
In Coffea canephora, a direct somatic embryogenesis (SE) protocol has been established by pretreating plants with NAA and kinetin, followed by the induction of leaf explants in a liquid medium with BA. Through a transcriptomic analysis of 10 key moments of the induction of SE in C. canephora, we were able to establish that the transcriptional responses of this process are divided into four stages. These stages correspond to the pretreatment, characterized by the positive regulation of genes associated with cell wall remodeling, flavonoid biosynthesis, and antioxidant activity that prepare the explants for the intense cellular activity that represents the induction of SE. During the first few hours, the early response to induction occurs, characterized by the highest number of differentially expressed genes, most related to the response to multiple stimuli. At 24 h, a late response begins with the upregulation of genes related to energy production and the biosynthesis of amino acids. Finally, WOX, BBM, and ABI3 genes are upregulated during the embryogenic response. The downregulation of genes related to the circadian cycle, photomorphogenesis, photosynthesis, and chloroplast components were observed throughout the process. The detailed analysis of the primary transcriptional responses that occur during the SE of C. canephora helps us to clarify how auxins and cytokinins orchestrate the integration of different networks of plant metabolism and lead to the development of somatic embryos. Full article
(This article belongs to the Special Issue Plant Tissue Culture: Genomics, Proteomics, Transcriptomics, and Metabolomics Approaches)
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Review

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15 pages, 1623 KiB  
Review
Current Advancement and Future Prospects in Simplified Transformation-Based Plant Genome Editing
by Xueying Han, Zhaolong Deng, Huiyun Liu and Xiang Ji
Plants 2025, 14(6), 889; https://doi.org/10.3390/plants14060889 - 12 Mar 2025
Viewed by 1237
Abstract
Recent years have witnessed remarkable progress in plant biology, driven largely by the rapid evolution of CRISPR/Cas-based genome editing (GE) technologies. These tools, including versatile CRISPR/Cas systems and their derivatives, such as base editors and prime editors, have significantly enhanced the universality, efficiency, [...] Read more.
Recent years have witnessed remarkable progress in plant biology, driven largely by the rapid evolution of CRISPR/Cas-based genome editing (GE) technologies. These tools, including versatile CRISPR/Cas systems and their derivatives, such as base editors and prime editors, have significantly enhanced the universality, efficiency, and convenience of plant functional genomics, genetics, and molecular breeding. However, traditional genetic transformation methods are essential for obtaining GE plants. These methods depend on tissue culture procedures, which are time-consuming, labor-intensive, genotype-dependent, and challenging to regenerate. Here, we systematically outline current advancements in simplifying plant GE, focusing on the optimization of tissue culture process through developmental regulators, the development of in planta transformation methods, and the establishment of nanomaterial- and viral vector-based delivery platforms. We also discuss critical challenges and future directions for achieving genotype-independent, tissue culture-free plant GE. Full article
(This article belongs to the Special Issue Plant Tissue Culture: Genomics, Proteomics, Transcriptomics, and Metabolomics Approaches)
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