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Latest Research on Plant Genomics and Genome Editing, 2nd Edition
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Latest Research on Plant Genomics and Genome Editing, 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: closed (31 May 2025) | Viewed by 1861

Special Issue Editor

Dr. Fabrizio Carbone

E-Mail Website
Guest Editor
Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
Interests: genomics; bioinformatics; plant biology; NBT; GWAS; olive breeding; photoperception; ripening; flowering; secondary metabolites
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Scientists are able to edit genomes efficiently and cost-effectively thanks to the many high-quality reference genome sequences that are currently available. Zinc finger nucleases (ZFNs), transcription activator-like effector-based nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system have successfully been employed to edit numerous individual genes in many organisms, and CRISPR-edited plants are now on the market. The CRISPR-Cas system has been widely used to edit genetic elements in genomes for various applications—not only crop improvement but also many gene therapy studies. For this Special Issue, we cordially invite scientists from around the world to contribute their cutting-edge research on plant genomics and genome editing. We welcome the submission of original research articles and short communications contributing to the advancement of genomics and genome editing, including techniques, applications, trait development, and enabling database as well as computational software. We are also inviting scientists to write reviews for this Special Issue.

Dr. Fabrizio Carbone
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. 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

  • next-generation sequencing
  • structural and functional genomics
  • SNPs
  • miRNA
  • LncRNA
  • CRISPR/Cas9
  • TALEN
  • genome editing

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Published Papers (3 papers)

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28 pages, 12948 KiB  
Article
Tissue- and Condition-Specific Biosynthesis of Ascorbic Acid in Glycine max L.: Insights from Genome-Wide Analyses of Pathway-Encoding Genes, Expression Profiling, and Mass Fraction Determination
by Shahid Aziz, Thais Andrade Germano, Maria Adriele dos Santos de Sousa Do Nascimento, Clesivan Pereira dos Santos, Birgit Arnholdt-Schmitt, Maria Raquel Alcântara de Miranda, Mara Menezes de Assis Gomes, Luis Miguel Mazorra Morales, Ricardo Antônio Ayub, Jurandi Gonçalves de Oliveira and José Hélio Costa
Int. J. Mol. Sci. 2025, 26(10), 4678; https://doi.org/10.3390/ijms26104678 - 14 May 2025
Viewed by 359
Abstract
Ascorbic acid (AsA) is an essential plant metabolite that acts primarily as an antioxidant, regulates cell division and elongation, and enhances stress tolerance. Despite its crucial physiological role, the biosynthesis of AsA in G. max, a major crop of significant commercial importance, [...] Read more.
Ascorbic acid (AsA) is an essential plant metabolite that acts primarily as an antioxidant, regulates cell division and elongation, and enhances stress tolerance. Despite its crucial physiological role, the biosynthesis of AsA in G. max, a major crop of significant commercial importance, remains largely unexplored. This gap highlights the need for a thorough investigation of AsA biosynthesis pathways and their role in optimizing the nutritional value and stress tolerance of soybeans. This study identified 41 key genes linked to four AsA biosynthesis pathways in G. max, highlighting specific gene duplications compared to Arabidopsis. Their expression levels were assessed by analyzing a diverse set of RNA-Seq data from the NCBI database. Additionally, to cross-validate the expression levels of genes and the accumulation levels of AsA in the principal tissues, G. max plants were grown under controlled conditions following the protocols from selected RNA-seq experiments. Genes associated with the D-mannose/L-galactose pathway exhibited ubiquitous expression, and the expression patterns of genes from alternative pathways reflected their responsiveness to specific tissues or environmental conditions. Germination and leaf development were accompanied by strong expression of gene members from all pathways, whereas leaf aging was characterized by downregulation. Specific gene members, such as GMP_2a (D-mannose/L-galactose pathway), GulLO_1f (L-gulose pathway), and MIOX_3a (Myo-inositol pathway) were highly stress-responsive and linked to stress-resistant genotypes and cultivars. Consistent with gene expression analyses, the quantification of AsA revealed the highest mass fractions in young leaves and germinating seeds. However, AsA mass fractions were significantly reduced or unchanged under stress conditions, depending on the type of stress and the duration of exposure. Overall, this study validated the relevance of AsA biosynthesis pathways in soybeans, highlighting key genes that could be targeted to enhance stress tolerance and improve ascorbate production, thereby boosting the nutritional value of soybeans. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing, 2nd Edition)
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23 pages, 4937 KiB  
Article
Suitability of Real-Time PCR Methods for New Genomic Technique Detection in the Context of the European Regulations: A Case Study in Arabidopsis
by Caroline Bedin Zanatta, Frank Narendja, Hilana El Jawhary, Gretta Abou-Sleymane, Saminathan Subburaj, Rubens Onofre Nodari and Sarah Zanon Agapito-Tenfen
Int. J. Mol. Sci. 2025, 26(7), 3308; https://doi.org/10.3390/ijms26073308 - 2 Apr 2025
Viewed by 637
Abstract
PCR methods are widely applied for the detection of genetically modified organisms (GMOs) in Europe, facilitating compliance with stringent regulatory requirements and enabling the accurate identification and quantification of genetically modified traits in various crops and foodstuffs. This manuscript investigates the suitability of [...] Read more.
PCR methods are widely applied for the detection of genetically modified organisms (GMOs) in Europe, facilitating compliance with stringent regulatory requirements and enabling the accurate identification and quantification of genetically modified traits in various crops and foodstuffs. This manuscript investigates the suitability of real-time PCR methods for detecting organisms generated through new genomic techniques (NGTs), specifically focusing on a case study using Arabidopsis thaliana as a model gene-edited plant. Given the complexities of European regulations regarding genetically modified organisms (GMOs) and the classification of gene-edited plants, there is a pressing need for robust detection methods. Our study highlights the development and validation of a novel single-plex real-time PCR method targeting a specific single nucleotide polymorphism (SNP) in the grf1-3 gene modified using CRISPR-Cas9 technology. We emphasize the effectiveness of locked nucleic acid (LNA)-modified primers in improving specificity. The results demonstrate that while the grf1-3 LNA method successfully detected and quantified gene-edited Arabidopsis DNA, achieving absolute specificity remains a challenge. This study also addresses the significance of the cross-laboratory method for validation, demonstrating that the method developed for an SNP-modified allele can be performed in accordance with the precision and trueness criteria established by the European Network of GMO Laboratories (ENGL). Furthermore, we call for continued collaboration among regulatory agencies, academia, and industry stakeholders to refine detection strategies. This proactive approach is essential not only for regulatory compliance but also for maintaining public trust in the safe integration of gene-edited organisms into food products. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing, 2nd Edition)
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16 pages, 2136 KiB  
Article
Salt-Resilient Cowpeas: Early Identification Through Growth Parameters and Gene Expression at Germination Stage
by Patrícia Afonso, Isaura Castro and Márcia Carvalho
Int. J. Mol. Sci. 2025, 26(5), 1892; https://doi.org/10.3390/ijms26051892 - 22 Feb 2025
Cited by 1 | Viewed by 518
Abstract
Soil salinity is one of the most severe impacts of climate change, negatively affecting plant growth and development. Seed germination and seedling emergence are among the most critical stages susceptible to salt stress, making it important to explore them to identify the most [...] Read more.
Soil salinity is one of the most severe impacts of climate change, negatively affecting plant growth and development. Seed germination and seedling emergence are among the most critical stages susceptible to salt stress, making it important to explore them to identify the most resilient accessions for crop yield improvement. Cowpea (Vigna unguiculata L. Walp.) is an important crop due to its ability to fix atmospheric nitrogen, improving soil health, and its high protein content. The main objectives of this study were to screen salt-resilient cowpea accessions from a worldwide collection and to evaluate cowpea responses to salt stress at germination stage through gene expression analysis. A total of 40 cowpea accessions from sixteen different countries were subjected to two treatments: control (water) and salt stress (150 mM NaCl solution). The seeds germinated, and the seedlings grew for ten days. The germination and growth parameters and lipid peroxidation quantification were determined. The results revealed significant differences in all parameters among accessions and treatments. A high variation in salt responses was detected among accessions, allowing the selection of five accessions (Co_2, Co_4, Co_21, Co_30, Co_31) as resilient to salt stress at germination stage. Subsequently, two salt stress-related genes (DREB2 and VuEXO) were evaluated through qPCR, revealing genotype-dependent regulation. These results provide valuable insights for the early selection of salt-resilient cowpea accessions, which may be considered for the development of improved and new varieties in the future. Full article
(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing, 2nd Edition)
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