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Developing Methods and Molecular Basis in Plant Biotechnology
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Developing Methods and Molecular Basis in Plant Biotechnology

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 June 2025 | Viewed by 6382

Special Issue Editors

Dr. Wojciech Makowski

E-Mail Website
Guest Editor
Department of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
Interests: plant biotechnology; plant physiology; green chemistry; plant genetic; plant proteomic
Prof. Dr. Mateusz Labudda

E-Mail Website
Guest Editor
Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
Interests: molecular, biochemical, and physiological mechanisms of plant responses to pathogens and pests especially reactive oxygen and nitrogen species; enzymatic and non-enzymatic antioxidants; sugars as signaling molecules; regulation of proteolysis and nitrogen metabolism; additional research topics concern the plant abiotic stress especially metallic trace elements and mechanisms of combined stresses
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. Nowadays, 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 looking for new biotechnological solutions for people 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
Dr. Mateusz Labudda
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. 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 (5 papers)

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Research

21 pages, 17782 KiB  
Article
Enhancing Passion Fruit Resilience: The Role of Hariman in Mitigating Viral Damage and Boosting Productivity in Organic Farming Systems
by José Leonardo Santos-Jiménez, Caroline de Barros Montebianco, Mariana Collodetti Bernardino, Eliana Barreto-Bergter, Raul Castro Carriello Rosa and Maite Freitas Silva Vaslin
Int. J. Mol. Sci. 2025, 26(5), 2177; https://doi.org/10.3390/ijms26052177 - 28 Feb 2025
Viewed by 463
Abstract
This study investigates the molecular mechanisms by which Hariman mitigates damage and productivity losses caused by Cucumber Aphid-Borne Mosaic Virus (CABMV) in the passion fruit genotypes ‘FB300’ and ‘H09-110/111’ under greenhouse and field conditions in Rio de Janeiro, Brazil. Hariman treatment induced the [...] Read more.
This study investigates the molecular mechanisms by which Hariman mitigates damage and productivity losses caused by Cucumber Aphid-Borne Mosaic Virus (CABMV) in the passion fruit genotypes ‘FB300’ and ‘H09-110/111’ under greenhouse and field conditions in Rio de Janeiro, Brazil. Hariman treatment induced the upregulation of key defense genes and phytohormones in response to CABMV infection, enabling treated plants to counteract virus-induced developmental impairments effectively. The relative accumulation of CABMV and disease severity were significantly reduced, with treated plants showing no decline in growth parameters such as height, leaf count, flower production, or fruit set. Over 18 months, total productivity increased by 65.7% and 114% for ‘FB300’ and by 44% and 80% for ‘H09-110/111’ after one and two applications of Hariman, respectively. Notably, infected plants treated with Hariman outperformed healthy plants grown under similar conditions, underscoring the biofertilizer’s dual role in promoting plant growth while enhancing resistance to biotic stressors. These findings indicate that Hariman stimulates robust growth and induces the expression of the defense-related genes PR-3, SOD, POD12, PAL, and LOX2 alongside the expression of the phytohormone-associated genes SAUR20 and GA2ox across different passion fruit genotypes. The adoption of these sustainable technologies holds significant potential for enhancing passion fruit productivity in the face of diseases that severely threaten this crop. Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology)
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16 pages, 2950 KiB  
Article
Functional Characterization of β-Glucuronidase Genes Involved in Baicalein Biosynthesis from Scutellaria baicalensis Based on Transcriptome Analysis
by Xin Zuo, Ping Li, Guangxi Ren, Zhenfang Bai, Dan Jiang and Chunsheng Liu
Int. J. Mol. Sci. 2025, 26(5), 1793; https://doi.org/10.3390/ijms26051793 - 20 Feb 2025
Cited by 1 | Viewed by 445
Abstract
Baicalein is a unique flavonoid compound with important pharmacological activities, derived from Scutellaria baicalensis Georgi. Baicalein, as the aglycone of baicalin, is a key form for exerting pharmacological activity in vivo. β-glucuronidases (GUSs) are the enzymes involved in the conversion of baicalin [...] Read more.
Baicalein is a unique flavonoid compound with important pharmacological activities, derived from Scutellaria baicalensis Georgi. Baicalein, as the aglycone of baicalin, is a key form for exerting pharmacological activity in vivo. β-glucuronidases (GUSs) are the enzymes involved in the conversion of baicalin to baicalein. In this study, the content of baicalein in S. baicalensis was significantly increased by 20.44% after treatment with 5% PEG6000. Seven GUSs from the glycoside hydrolase 79 family were identified through comparative transcriptome analysis. Among them, GUS1 and GUS2 were confirmed to have catalytic activity in converting baicalin to baicalein in prokaryotic and eukaryotic systems. The correlation analysis further revealed a significant positive correlation of 0.962 (p < 0.01) between the expression of GUS2 and baicalein content in six different sources of S. baicalensis. Interestingly, the presence of variable sites in the GUS1 and GUS2 genes significantly affected their catalytic efficiency in the S. baicalensis samples from the six geographic origins. These findings also provide valuable GUS biological enzyme resources for the effective synthesis of baicalein and offer new insights into the accumulation pattern of baicalein in S. baicalensis. Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology)
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19 pages, 3239 KiB  
Article
Reynoutria japonica Houtt. Transformed Hairy Root Cultures as an Effective Platform for Producing Phenolic Compounds with Strong Bactericidal Properties
by Wojciech Makowski, Aleksandra Królicka, Krzysztof Hinc, Agnieszka Szopa, Paweł Kubica, Julia Sroka, Barbara Tokarz and Krzysztof Michał Tokarz
Int. J. Mol. Sci. 2025, 26(1), 362; https://doi.org/10.3390/ijms26010362 - 3 Jan 2025
Viewed by 1245
Abstract
Reynoutria japonica Houtt. is the source of various phenolic compounds: phenolic acids, flawan-3-ols, and stilbenes, with a broad range of biological activity. The rhizome (underground organ of these plants) is abundant in secondary metabolites but, in natural conditions, may accumulate various toxic substances [...] Read more.
Reynoutria japonica Houtt. is the source of various phenolic compounds: phenolic acids, flawan-3-ols, and stilbenes, with a broad range of biological activity. The rhizome (underground organ of these plants) is abundant in secondary metabolites but, in natural conditions, may accumulate various toxic substances (such as heavy metals) from the soil. The principal objective of this research was to produce transformed cultures of R. japonica hairy roots that would serve as a valuable source of phenolic compounds, independent of environmental resources. The transformation was performed using a variety of wild strains of Rhizobium rhizogenes bacteria, of which only strain A4 (ATCC 31798) proved effective. The molecular characterization of transformed clones was performed using PCR. The biometric parameters (growth index and dry weight content), phenolic compounds accumulation (DAD-HPLC), antioxidant capacity (DPPH, CUPRAC), and bactericidal properties against Staphylococcus aureus with various sensitivity to antibiotics were evaluated. Two obtained transformed clones (RJ 9 and 30) exhibited the incorporation of the entire bacterial T-DNA into genomic DNA, while clones RJ 10 and 11 demonstrated only the presence of the LT-DNA sequence. The results demonstrated an increase in flawan-3-ols (catechins) accumulation in hairy root tissue relative to non-transformed (NT) plants. Moreover, hairy roots exhibited enhanced antioxidant activity and bactericidal properties compared with NT roots and NT shoots, respectively. Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology)
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20 pages, 7012 KiB  
Article
Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats
by Yuanfang Fan, Sajad Hussain, Xianshu Wang, Mei Yang, Xiaojuan Zhong, Lei Tao, Jing Li, Yonghang Zhou and Chao Xiang
Int. J. Mol. Sci. 2025, 26(1), 294; https://doi.org/10.3390/ijms26010294 - 31 Dec 2024
Viewed by 981
Abstract
Soybean has outstanding nutritional and medicinal value because of its abundant protein, oil, and flavonoid contents. This crop has rich seed coat colors, such as yellow, green, black, brown, and red, as well as bicolor variants. However, there are limited reports on the [...] Read more.
Soybean has outstanding nutritional and medicinal value because of its abundant protein, oil, and flavonoid contents. This crop has rich seed coat colors, such as yellow, green, black, brown, and red, as well as bicolor variants. However, there are limited reports on the synthesis of flavonoids in the soybean seed coats of different colors. Thus, the seed coat metabolomes and transcriptomes of five soybean germplasms with yellow (S141), red (S26), brown (S62), green (S100), and black (S124) seed coats were measured. In this study, 1645 metabolites were detected in the soybean seed coat, including 426 flavonoid compounds. The flavonoids differed among the different-colored seed coats of soybean germplasms, and flavonoids were distributed in all varieties. Procyanidins A1, B1, B6, C1, and B2, cyanidin 3-O-(6″-malonyl-arabinoside), petunidin 3-(6″-p-coumaryl-glucoside) 5-glucoside, and malvidin 3-laminaribioside were significantly upregulated in S26_vs._S141, S62_vs._S141, S100_vs._S141, and S124_vs._S141 groups, with a variation of 1.43–2.97 × 1013 in terms of fold. The differences in the contents of cyanidin 3-O-(6″-malonyl-arabinoside) and proanthocyanidin A1 relate to the seed coat color differences of red soybean. Malvidin 3-laminaribioside, petunidin 3-(6″-p-coumaryl-glucoside) 5-glucoside, cyanidin 3-O-(6″-malonyl-arabinoside), and proanthocyanidin A1 affect the color of black soybean. The difference in the contents of procyanidin B1 and malvidin 3-glucoside-4-vinylphenol might be related to the seed coat color differences of brown soybeans. Cyanidin 3-gentiobioside affects the color of green soybean. The metabolomic–transcriptomic combined analysis showed that flavonoid biosynthesis is the key synthesis pathway for soybean seed color formation. Transcriptome analysis revealed that the upregulation of most flavonoid biosynthesis genes was observed in all groups, except for S62_vs._S141, and promoted flavonoid accumulation. Furthermore, CHS, CHI, DFR, FG3, ANR, FLS, LAR, and UGT88F4 exhibited differential expression in all groups. This study broadens our understanding of the metabolic and transcriptomic changes in soybean seed coats of different colors and provides new insights into developing bioactive substances from soybean seed coats. Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology)
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18 pages, 2597 KiB  
Article
Characterization of the IAA-Producing and -Degrading Pseudomonas Strains Regulating Growth of the Common Duckweed (Lemna minor L.)
by Tatjana Popržen, Ivan Nikolić, Dijana Krstić-Milošević, Branka Uzelac, Milana Trifunović-Momčilov, Marija Marković and Olga Radulović
Int. J. Mol. Sci. 2023, 24(24), 17207; https://doi.org/10.3390/ijms242417207 - 7 Dec 2023
Cited by 6 | Viewed by 2064
Abstract
The rhizosphere represents a center of complex and dynamic interactions between plants and microbes, resulting in various positive effects on plant growth and development. However, less is known about the effects of indole-3-acetic acid (IAA) on aquatic plants. In this study, we report [...] Read more.
The rhizosphere represents a center of complex and dynamic interactions between plants and microbes, resulting in various positive effects on plant growth and development. However, less is known about the effects of indole-3-acetic acid (IAA) on aquatic plants. In this study, we report the characterization of four Pseudomonas strains isolated from the rhizosphere of the common duckweed (Lemna minor) with IAA-degradation and -utilization ability. Our results confirm previous reports on the negative effect of IAA on aquatic plants, contrary to the effect on terrestrial plants. P. putida A3-104/5 demonstrated particularly beneficial traits, as it exhibited not only IAA-degrading and -producing activity but also a positive effect on the doubling time of duckweeds in the presence of IAA, positive chemotaxis in the presence of IAA, increased tolerance to oxidative stress in the presence of IAA and increased biofilm formation related to IAA. Similarly, P. gessardii C31-106/3 significantly shortened the doubling time of duckweeds in the presence of IAA, while having a neutral effect in the absence of IAA. These traits are important in the context of plant–bacteria interactions and highlight the role of IAA as a common metabolite in these interactions, especially in aquatic environments where plants are facing unique challenges compared to their terrestrial counterparts. We conclude that IAA-degrading and -producing strains presented in this study might regulate IAA effects on aquatic plants and confer evolutionary benefits under adverse conditions (e.g., under oxidative stress, excess of IAA or nutrient scarcity). Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology)
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