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Developing Methods and Molecular Basis in Plant Biotechnology: 2nd Edition
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Developing Methods and Molecular Basis in Plant Biotechnology: 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 1270

Special Issue Editor

Dr. Wojciech Makowski

E-Mail Website
Guest Editor
Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, al. Mickiewicza 21, 31-120 Krakow, Poland
Interests: plant biotechnology; plant physiology; green chemistry; plant genetic transformation; plant proteomic
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant biotechnology is one of the fastest-growing disciplines in the field of life sciences and involves many tools and techniques as well as molecular screening and genetic manipulation to obtain profitable or appropriable plants/plant products. Currently, the use of biotechnological techniques in improving the tolerance/resistance of plants to environmental stresses and plant protection products is particularly popular. Furthermore, in numerous research centers, plant biotechnologists are working to enhance the features of wood for the paper, pulp, and biofuel industries, and they are looking for new biotechnological solutions for human and animal nutrition, phytoremediation, and phytopharmacy applications.

In this Special Issue, “Developing Methods and Molecular Basis in Plant Biotechnology”, we welcome original research articles and reviews presenting novel findings in model, crop, and medical plant biotechnology. Manuscripts should be focused on molecular research with regard to both developing methods for carrying out plant biotechnology research and basic science issues.

The following are examples of topics within the scope of this Special Issue:

  • Broad aspects of plant genetic transformation using various methods;
  • Findings in plant genetics, proteomics, metabolomics, etc.;
  • Studies focused on the molecular and biochemical basis of stress in plants;
  • Other topics related to plant biotechnology and molecular research.

Dr. Wojciech Makowski
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 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 biotechnology
  • plant genetics
  • plant proteomics
  • plant metabolomics
  • stress

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Published Papers (2 papers)

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17 pages, 3193 KB  
Article
Complete Chloroplast Genome Characteristics and Phylogenetic Analysis of Brassica juncea L.
by Shenyue Tang, Juan Liu, Ziyi Zhu, Xingcai An, Junyuan Dong, Xiahong Luo, Changli Chen, Tingting Liu, Lina Zou, Shaocui Li and Xia An
Int. J. Mol. Sci. 2026, 27(6), 2882; https://doi.org/10.3390/ijms27062882 - 23 Mar 2026
Viewed by 326
Abstract
Yeyong mustard is a mustard vegetable belonging to the Brassicaceae family and the Brassica genus. This study assembled, annotated, and analyzed the chloroplast genome of Brassica juncea L., aiming to clarify its systematic evolutionary relationship with other cruciferous plants. The study used the [...] Read more.
Yeyong mustard is a mustard vegetable belonging to the Brassicaceae family and the Brassica genus. This study assembled, annotated, and analyzed the chloroplast genome of Brassica juncea L., aiming to clarify its systematic evolutionary relationship with other cruciferous plants. The study used the Illumina NovaSeq 6000 platform to sequence the entire chloroplast genome of leaf mustard, and systematically analyzed its genome structure, repeat sequences, nucleic acid diversity, and codon preferences using bioinformatics methods. At the same time, the phylogenetic relationships were constructed by combining the leaf chloroplast genome sequences of other cruciferous plants. The results showed that the chloroplast genome of leaf mustard had a total length of 153,490 bp and a GC content of 36.36%, exhibiting a typical tetrad structure; a total of 132 coding genes were annotated, including 87 mRNA genes, 37 tRNA genes, and eight rRNA genes, and no pseudogenes were found. Codon preference analysis shows that leucine (Leu) has the highest frequency of use, with 32 codons having a relative synonymous codon usage (RSCU) greater than 1, mostly ending in A or U; there are 37 scattered repetitive sequences and 315 simple repetitive sequences in the genome. Ka/Ks analysis showed that the chloroplast genes of leaf mustard were subjected to purification selection as a whole, while genes such as nadhF and petD showed positive selection, which is speculated to be related to adaptive evolution. The results of the phylogenetic analysis further confirm that the chloroplast genome of leaf mustard has a typical tetrad structure and is relatively conserved. It is most closely related to mustard greens in terms of evolutionary relationship, followed by Brassica plants such as nori and turnip, and is also closely related to Brassica plants such as European rapeseed. This study elucidated the conservative characteristics and evolutionary patterns of the chloroplast genome in mustard leaves, providing theoretical support for the phylogenetic research of the Brassicaceae family and the development and utilization of germplasm resources. Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology: 2nd Edition)
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27 pages, 98177 KB  
Article
Reference Gene Stability in Agrostemma githago Using Quantitative Real-Time PCR
by Monika Bielecka, Bartosz Pencakowski, Marta Stafiniak, Weronika Kozłowska, Michał Dziwak, Katarzyna Nowis, Łukasz Łaczmański and Adam Matkowski
Int. J. Mol. Sci. 2026, 27(2), 889; https://doi.org/10.3390/ijms27020889 - 15 Jan 2026
Cited by 1 | Viewed by 474
Abstract
Quantitative real-time PCR (qPCR) remains a cornerstone method for analyzing gene expression due to its high sensitivity, specificity, and reproducibility. However, for reliable results in relative quantification studies, the choice of an appropriate reference gene is critical to ensure accurate normalization. The expression [...] Read more.
Quantitative real-time PCR (qPCR) remains a cornerstone method for analyzing gene expression due to its high sensitivity, specificity, and reproducibility. However, for reliable results in relative quantification studies, the choice of an appropriate reference gene is critical to ensure accurate normalization. The expression of commonly used reference genes can vary depending on developmental stage and experimental conditions, making their validation essential. To date, no validated reference genes have been reported for Agrostemma githago L. (corn cockle, Caryophyllaceae). To facilitate research on genes involved in natural product biosynthesis and specialized metabolism regulation, we aimed to identify the most stable reference genes across various plant organs and cultivation conditions of this species. Drawing on previous literature, we have selected seven housekeeping genes widely used for evaluation: actin, β-tubulin, elongation factor 1α, glyceraldehyde-3-phosphate dehydrogenase, histone H3, translation elongation factor 1, and eukaryotic translation initiation factor 5A1 (for which two primer sets were tested). The nucleotide sequences of these potential reference genes were identified from the A. githago transcriptome. Using qRT-PCR, transcript levels of seven potential reference genes were estimated in 40 different A. githago samples, including 25 in vitro samples under various treatment conditions and 15 soil-grown samples representing A. githago organs in different developmental stages. Expression stability of candidate reference genes was assessed using the RefFinder platform, which combines four commonly applied statistical algorithms: geNorm, NormFinder, BestKeeper, and the comparative Δ-Ct method. The results revealed that the selection of optimal reference genes varied based on the particular organ, developmental stage and condition being examined. TIF5A1-2 (one of the two primer pairs tested) and GAPHD consistently exhibited the most stable expression under various conditions in vitro. EF1α and H3 exhibited superior performance across different organs of soil-grown plants. Moreover, our integrated analysis enabled the identification of the two most stable, universal reference genes suitable for normalization in A. githago under all tested conditions—H3 and TIF5A1-2. Our work provides a robust foundation for future transcriptomic and functional studies of the specialized metabolism of A. githago and other related species. Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology: 2nd Edition)
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