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Molecular Research on Plant Breeding
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Molecular Research on Plant Breeding

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 (20 March 2026) | Viewed by 2230

Special Issue Editors

Dr. Hélia Cardoso

E-Mail Website
Guest Editor
MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Escola de Ciências e Tecnologia, Departamento de Biologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
Interests: plant morphogenesis (adventitious rooting and somatic embryogenesis); in vitro plant propagation; abiotic stress response (transcriptomic/proteomic approach); plant breeding (marker-assisted selection)
Special Issues, Collections and Topics in MDPI journals
Dr. Sandra Correia

E-Mail Website
Guest Editor
InovPlantProtect, Estrada de Gil Vaz, Apartado 72, 7351-901 Elvas, Portugal
Interests: plant micropropagation and in vitro-induced morphogenesis; plant stress responses; cellular and molecular biology (transcriptomics and proteomics)
Special Issues, Collections and Topics in MDPI journals
Dr. Isaura Castro

E-Mail Website
Guest Editor
Department of Genetics and Biotechnology, School of Life and Environmental Sciences, Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal
Interests: plant genetic resources di-versity; plant (a)biotic stress tolerance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant breeding is the science of enhancing plants to develop desirable traits, such as higher yield and quality, stress tolerance, disease resistance, and environmental adaptability. The integration of recent advancements in biotechnology, plant genomics, and molecular marker applications with traditional breeding practices has established the foundation of molecular plant breeding. This interdisciplinary field is revolutionizing crop improvement by creating new plant varieties tailored to meet specific agricultural, ecological, and consumer-related needs. The identification of key regulatory genes and pathways opens exciting opportunities for breeding or engineering crops with enhanced stress tolerance or other important quality traits.

Leading by Prof. Dr. Hélia Cardoso, Dr. Sandra Correia, Dr. Isaura Castro and assisting by our Topical Advisory Panel Member Dr. Lénia Rodrigues (University of Évora), this Special Issue aims to highlight innovative research that deepens our understanding of molecular approaches to support traditional breeding programs. We welcome submissions of original research articles, reviews, mini-reviews, and methods papers, including but not limited to, the following:

  • Studies on molecular markers for marker-assisted selection.
  • Transcriptomic approaches exploring plant molecular responses to environmental challenges.
  • Proteomics, metabolomics, or epigenomics research to unravel the complexity of plant development and adaptation.
  • Applications of gene-editing technologies, such as CRISPR/Cas9, for targeting specific plant traits.

Dr. Hélia Cardoso
Dr. Sandra Correia
Dr. Isaura Castro
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 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 breeding
  • proteomics
  • metabolomics
  • epigenomics
  • gene editing

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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24 pages, 2189 KB  
Article
Integrating Metabolic and Gene Expression Profiling of Glucosinolate Biosynthesis Under Drought Stress in Brassica oleracea
by Hajer Ben Ammar, Souhir Kabtni, Donata Arena, Marwen Amari, Nicolas Al Achkar, Ferdinando Branca and Sonia Marghali
Int. J. Mol. Sci. 2026, 27(3), 1598; https://doi.org/10.3390/ijms27031598 - 6 Feb 2026
Viewed by 628
Abstract
Drought stress induces pronounced metabolic and transcriptional reprogramming of glucosinolate (GLS) biosynthesis in Brassica oleracea. An integrative approach combining HPLC-based quantification of individual GLSs, quantitative real-time PCR of core biosynthetic and regulatory genes, correlation-based network analysis, and in silico promoter characterization was [...] Read more.
Drought stress induces pronounced metabolic and transcriptional reprogramming of glucosinolate (GLS) biosynthesis in Brassica oleracea. An integrative approach combining HPLC-based quantification of individual GLSs, quantitative real-time PCR of core biosynthetic and regulatory genes, correlation-based network analysis, and in silico promoter characterization was applied to evaluate drought responses across genetically diverse accessions. Drought triggered strong, accession-specific shifts in GLS composition, with sinigrin content increasing from 35.9% to 55.1% in BR1 and glucoerucin reaching up to 80.2% in CCP1, while indolic GLSs such as glucobrassicin and neoglucobrassicin accounted for >75% of total GLSs in CV2 and CCP3. Hierarchical clustering separated accessions into four distinct drought response clusters independent of morphotype. Correlation analysis revealed drought-induced rewiring of GLS interdependencies, characterized by strengthened positive associations among aliphatic GLSs (r > 0.75). Gene expression profiling identified conserved MYB-centered regulatory modules (MYB28, MYB29, MYB34, MYB122) alongside strong accession-specific induction of CYP79F1 (up to 6.3-fold), FMOGS-OX5 (up to 4.8-fold), and ST5a (up to 5.1-fold). Promoter analysis revealed enrichment of ABA- and stress-responsive cis-regulatory elements. These findings delineate a genotype-dependent regulatory framework underlying GLS plasticity and identify quantitative metabolic and transcriptional markers relevant for breeding drought-resilient Brassica cultivars. Full article
(This article belongs to the Special Issue Molecular Research on Plant Breeding)
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14 pages, 2107 KB  
Article
Simple Sequence Repeat-Based Genetic Diversity Analysis of Alfalfa Varieties
by Jie Wang, Xiaoli Wei, Changying Guo, Chengti Xu, Yuanyuan Zhao, Xiaojian Pu and Wei Wang
Int. J. Mol. Sci. 2025, 26(11), 5246; https://doi.org/10.3390/ijms26115246 - 29 May 2025
Cited by 4 | Viewed by 1104
Abstract
Alfalfa, as a high-quality forage resource, has high nutritional value. Due to the high phenotypic similarity among its varieties and the susceptibility to environmental influences, challenges are encountered in variety identification and breeding. In this study, 23 simple sequence repeat (SSR) markers were [...] Read more.
Alfalfa, as a high-quality forage resource, has high nutritional value. Due to the high phenotypic similarity among its varieties and the susceptibility to environmental influences, challenges are encountered in variety identification and breeding. In this study, 23 simple sequence repeat (SSR) markers were screened to distinguish 49 alfalfa varieties, among which 21 SSR markers showed polymorphic fragments. The results indicated that these 21 markers were highly polymorphic, with an average of 5.91 alleles per SSR marker locus and an average polymorphic information content (PIC) of 0.66, suggesting a strong discriminatory efficiency. The results of a population genetic diversity analysis showed that there was a relatively high level of genetic diversity among the tested materials. The analysis of molecular variance (AMOVA) results indicated that the genetic variation within the population of the 49 alfalfa germplasm samples was the main source of the total variation. The results of genetic distance and genetic identity analyses showed that the genetic relationship between population 1 and population 4 was the most distant, while the relationship between population 2 and population 3 was the closest. The cluster analysis results showed that samples S16 and S55 formed a separate branch; that is, there were two main genetic subgroups. These results confirm that SSR markers are effective tools for genetic characterization and precise discrimination of alfalfa varieties and have important application values in breeding, variety registration, and germplasm resource conservation. Full article
(This article belongs to the Special Issue Molecular Research on Plant Breeding)
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