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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 January 2026 | Viewed by 8254

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Dr. Fabrizio Carbone

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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
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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 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.

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Keywords

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

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Published Papers (6 papers)

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Research

18 pages, 5504 KB

Open AccessArticle

The Complete Chloroplast Genome and the Phylogenetic Analysis of Panicum bisulcatum (Thumb.) (Poaceae)

by Yuan Gao, Yutong Cai, Huifeng Wang, Zhihui Tian and Zhaofeng Huang

Int. J. Mol. Sci. 2026, 27(1), 135; https://doi.org/10.3390/ijms27010135 - 22 Dec 2025

Viewed by 167

Abstract

The chloroplast (cp) genome of Panicum bisulcatum (Thumb.), a significant agricultural weed, was sequenced and characterized to elucidate its genomic architecture, evolutionary dynamics, and phylogenetic relationships. The complete cp genome was assembled as a circular DNA molecule of 138,489 bp, exhibiting a typical quadripartite structure comprising a large single-copy (LSC, 82,260 bp), a small single-copy (SSC, 12,569 bp), and a pair of inverted repeats (IR, 21,830 bp each) regions. It encodes 135 genes, including 89 protein-coding genes, 49 tRNAs, and 8 rRNAs. Functional annotation revealed that most genes are involved in photosynthesis and genetic system. A total of 51 simple sequence repeats (SSRs) and 62 long repeats (LRs) were identified, providing potential molecular markers. Comparative analysis of IR boundaries highlighted both conserved features and species-specific expansion/contraction events among Panicum species. Phylogenomic analysis robustly placed P. bisulcatum within the genus Panicum, showing a closest relationship with P. incomtum and confirming the monophyly of the genus. Furthermore, single nucleotide polymorphism (SNP) analysis with its closest relative, P. incomtum, revealed 4659 SNPs, with a dominance of synonymous substitutions, indicating the action of purifying selection. This study provides the first comprehensive cp genomic resource for P. bisulcatum, which will facilitate future studies in species identification, phylogenetic reconstruction, population genetics, and the development of sustainable management strategies for this weed. Full article

(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing, 2nd Edition)

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17 pages, 1549 KB

Open AccessArticle

Genetic Control of Grain Protein and Gluten Content: Winter vs. Spring Wheat

by Antonina A. Kiseleva, Anna V. Fedyaeva, Irina N. Leonova and Elena A. Salina

Int. J. Mol. Sci. 2025, 26(22), 11159; https://doi.org/10.3390/ijms262211159 - 18 Nov 2025

Viewed by 503

Abstract

Common wheat breeding programs prioritize the development of high grain protein content (GPC) varieties, as GPC influences milling efficiency and end-use quality. However, the molecular basis of protein and gluten accumulation in wheat grains remains insufficiently understood, particularly regarding genetic differences between spring and winter types. We analyzed 170 winter wheat varieties from diverse domestic and international breeding programs cultivated in the European part of Russia over two growing seasons. Genome-wide association study identified 26 markers linked to GPC and 23 to gluten content (p < 0.001), with the strongest associations on chromosomes 4A and 2D. Variation in NAM-A1 also significantly affected GPC: varieties with the NAM-A1d allele showed lower protein content than NAM-A1a/c carriers (p < 0.01). We combined associations identified here with our previous GWAS results for GPC in spring wheat and further compared them with 17 additional studies including both spring and winter varieties. This analysis highlighted loci on chromosomes 3DL, 5AL, and 6AS (confirmed in at least two previous studies) for marker-assisted selection to improve grain quality. The distribution of loci showed no clear distinction between spring and winter wheat, suggesting that, despite environmental and developmental differences, the genetic basis of protein accumulation is largely shared. Full article

(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing, 2nd Edition)

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28 pages, 2549 KB

Open AccessArticle

A 25K Wheat SNP Array Revealed the Genetic Diversity and Population Structure of Durum Wheat (Triticum turgidum subsp. durum) Landraces and Cultivars

by Lalise Ararsa, Behailu Mulugeta, Endashaw Bekele, Negash Geleta, Kibrom B. Abreha and Mulatu Geleta

Int. J. Mol. Sci. 2025, 26(15), 7220; https://doi.org/10.3390/ijms26157220 - 25 Jul 2025

Viewed by 2322

Abstract

Durum wheat, the world’s second most cultivated wheat species, is a staple crop, critical for global food security, including in Ethiopia where it serves as a center of diversity. However, climate change and genetic erosion threaten its genetic resources, necessitating genomic studies to support conservation and breeding efforts. This study characterized genome-wide diversity, population structure (STRUCTURE, principal coordinate analysis (PCoA), neighbor-joining trees, analysis of molecular variance (AMOVA)), and selection signatures (F_ST, Hardy–Weinberg deviations) in Ethiopian durum wheat by analyzing 376 genotypes (148 accessions) using an Illumina Infinium 25K single nucleotide polymorphism (SNP) array. A set of 7842 high-quality SNPs enabled the assessments, comparing landraces with cultivars and breeding populations. Results revealed moderate genetic diversity (mean polymorphism information content (PIC) = 0.17; gene diversity = 0.20) and identified 26 loci under selection, associated with key traits like grain yield, stress tolerance, and disease resistance. AMOVA revealed 80.1% variation among accessions, with no significant differentiation by altitude, region, or spike density. Landraces formed distinct clusters, harboring unique alleles, while admixture suggested gene flow via informal seed exchange. The findings highlight Ethiopia’s rich durum wheat diversity, emphasizing landraces as reservoirs of adaptive alleles for breeding. This study provides genomic insights to guide conservation and the development of climate-resilient cultivars, supporting sustainable wheat production globally. Full article

(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing, 2nd Edition)

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28 pages, 12948 KB

Open AccessArticle

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

Cited by 1 | Viewed by 1104

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, 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 KB

Open AccessArticle

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

Cited by 2 | Viewed by 2427

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 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 KB

Open AccessArticle

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 3 | Viewed by 1019

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 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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