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Plants
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Omics in Plant Development and Stress Responses
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Omics in Plant Development and Stress Responses

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 1424

Editors

Dr. Marta Gietler

E-Mail Website
Guest Editor
Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland
Interests: crops; abiotic stresses; proteome; plant signaling
Special Issues, Collections and Topics in MDPI journals
Dr. Joanna Szewińska

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: cereal crops; biotic and abiotic stresses; plant stress responses; cuticular wax biosynthesis

Special Issue Information

Dear Colleagues,

Plant growth, development, and productivity are closely regulated by intricate molecular networks that enable plants to respond and adapt to constantly changing environmental conditions. In the context of global climate change, it is increasingly important to understand how plants respond to both biotic and abiotic stresses in order to ensure crop resilience and sustainable agricultural production. Recent advancements in high-throughput omics technologies have created unprecedented opportunities to explore these processes at various regulatory levels.

This Special Issue of Plants, titled “Omics in Plant Development and Stress Responses,” aims to showcase cutting-edge research that utilizes omics-based approaches—including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and integrative multi-omics—to reveal the molecular mechanisms underlying plant development and stress adaptation. Contributions that address plant responses to abiotic stresses such as drought, salinity, temperature extremes, flooding, and nutrient imbalances, as well as biotic stresses caused by pathogens and pests, are particularly encouraged.

We welcome original research articles, reviews, and methodological studies focusing on model plants and crops. By integrating diverse omics datasets, this Special Issue seeks to enhance our understanding of the regulatory networks governing plant development and stress responses, providing valuable insights for crop improvement and climate-resilient agriculture. Submitted manuscripts must not be previously published or under evaluation for publication in another journal.

Dr. Marta Gietler
Dr. Joanna Szewińska
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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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 development
  • abiotic stress
  • biotic stress
  • plant signaling
  • plant stress responses
  • plant stress adaptation
  • stress-resilient crops
  • crop improvement
  • omics approaches
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • epigenomics
  • integrative multi-omics

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Published Papers (3 papers)

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Research

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22 pages, 5082 KB  
Article
Genome-Wide Characterization of Long Non-Coding RNAs Identifies Candidate Regulatory Networks During Modern Maize Breeding
by Zhongyu Wang, Yang Yang, Yating He, Ning Li and Changyu Li
Plants 2026, 15(12), 1772; https://doi.org/10.3390/plants15121772 - 8 Jun 2026
Viewed by 219
Abstract
Long non-coding RNAs (lncRNAs) have emerged as important regulatory molecules in plants, but their potential roles during modern maize breeding remain largely unexplored. This study systematically characterized lncRNA expression dynamics using transcriptome data from 137 maize inbred lines from different breeding eras in [...] Read more.
Long non-coding RNAs (lncRNAs) have emerged as important regulatory molecules in plants, but their potential roles during modern maize breeding remain largely unexplored. This study systematically characterized lncRNA expression dynamics using transcriptome data from 137 maize inbred lines from different breeding eras in China. We identified 18,023 lncRNAs transcripts, grouped by expression trends across historical breeding eras. Comparative analysis revealed 2228 differentially expressed lncRNAs transcripts (DElncRNAs) between modern (CN2000&10s) and early (CN1960&70s) accessions. By integrating WGCNA and cis-target analysis, we identified candidate lncRNAs and putative lncRNA-PCG associations that may be associated with maize plant architecture-related processes. Further, 771 DElncRNAs were predicted to be associated with 810 protein-coding genes, and these associated genes were significantly enriched in plant hormone signal transduction. Dual-luciferase reporter assays provided preliminary experimental support that lncrna.33063 and lncrna.33068 can repress the promoter activity of ZmPIF5.2 in a heterologous transient expression system. Furthermore, we constructed a putative ceRNA-related candidate interaction network consisting of lncRNA–miRNA–mRNA triplets that include 317 candidate miRNA-lncRNA pairs and 8325 candidate miRNA-mRNA pairs, with the associated mRNAs enriched in biological processes such as morphogenesis, stimulus response, and hormone metabolism. These findings provide a set of candidate lncRNAs and lncRNA-PCG associations for future functional validation and may offer useful clues for understanding the possible roles of lncRNAs in agronomic trait-related biological processes and maize molecular breeding. Overall, this study provides candidate genetic resources and a framework for future investigation of lncRNA-associated relationships potentially related to agronomic trait variation in maize. Full article
(This article belongs to the Special Issue Omics in Plant Development and Stress Responses)
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20 pages, 15979 KB  
Article
Functional Analysis of GhEXLB2 in Regulating Cotton Resistance to Verticillium Wilt
by Xuechi Li, Madad Allah, Xuehan Zhu, Junwei Wang, Ran Zhong, Jianting Feng, Haohua Chen, Manhong Wang, Fei Wang, Shandang Shi and Hongbin Li
Plants 2026, 15(11), 1616; https://doi.org/10.3390/plants15111616 - 25 May 2026
Viewed by 454
Abstract
Verticillium wilt (VW), caused by the soil-borne fungus Verticillium dahliae, is a major disease that markedly compromises both the yield and fiber quality of cotton. In this study, we explored the function and underlying mechanism of the cotton expansin gene GhEXLB2 in [...] Read more.
Verticillium wilt (VW), caused by the soil-borne fungus Verticillium dahliae, is a major disease that markedly compromises both the yield and fiber quality of cotton. In this study, we explored the function and underlying mechanism of the cotton expansin gene GhEXLB2 in response to VW infection. Expression profiling revealed that members of the GhEXL family exhibit distinct patterns across tissues and under various biotic and abiotic stresses. Notably, GhEXLB2, which encodes an extracellular protein, showed the strongest induction following V. dahliae challenge. Ectopic expression of GhEXLB2 in Arabidopsis thaliana promoted root elongation and root hair formation, and was associated with improved resistance to the pathogen. In contrast, silencing GhEXLB2 in cotton via virus-induced gene silencing (VIGS) led to pronounced vascular browning, increased pathogen recovery, and a lower level of disease resistance. In addition, RNA-seq profiling of GhEXLB2-silenced (VIGS) cotton plants revealed that most differentially expressed genes were enriched in pathways related to phytohormone signaling and plant–pathogen interactions, with salicylic acid (SA) signaling and WRKY transcription factors emerging as central regulatory components. Analysis of the GhEXLB2 promoter further identified multiple cis-acting elements associated with stress and hormone responsiveness. When integrated with protein–protein interaction (PPI) prediction data, these results suggest that GhEXLB2 may be modulated by a network of transcription factors and signaling pathways. Collectively, the evidence supports a positive association between GhEXLB2 and VW resistance. This study provides a framework for understanding expansin functions in cotton defense against VW. Full article
(This article belongs to the Special Issue Omics in Plant Development and Stress Responses)
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Review

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65 pages, 3093 KB  
Review
Decoding the Functional Proteome of Vitis: Past, Present, and Future
by Ivana Tomaz, Ana Jeromel, Darko Vončina, Ivanka Habuš Jerčić, Boris Lazarević, Iva Šikuten, Simona Hofer Geušić and Darko Preiner
Plants 2026, 15(9), 1314; https://doi.org/10.3390/plants15091314 - 24 Apr 2026
Viewed by 449
Abstract
Proteomic research in the genus Vitis has progressed from early biochemical studies of soluble proteins to high-resolution, quantitative analyses encompassing all major organs and derived products. This review provides a comprehensive synthesis of advances in grapevine and wine proteomics. In leaves, studies have [...] Read more.
Proteomic research in the genus Vitis has progressed from early biochemical studies of soluble proteins to high-resolution, quantitative analyses encompassing all major organs and derived products. This review provides a comprehensive synthesis of advances in grapevine and wine proteomics. In leaves, studies have revealed extensive remodeling of photosynthetic, antioxidant, and defense pathways under biotic (e.g., Plasmopara viticola, Erysiphe necator, Xylella fastidiosa, Candidatus Phytoplasma vitis) and abiotic stresses (drought, salinity, heat, light). Bud proteomics elucidated hormonal regulation and mechanisms of dormancy release, while root studies identified nitrate-dependent metabolic shifts and adaptive protein networks. Cell culture models enabled controlled investigation of elicitor responses, stilbene biosynthesis, and temperature-induced proteome changes. In berries, proteomics clarified developmental transitions from fruit set to ripening, emphasizing proteins related to secondary metabolism, vacuolar transport, and stress tolerance. Comparative analyses across cultivars and environments identified biomarkers linked to aroma, color, and texture. The wine proteome revealed selective persistence of grape-derived proteins (e.g., thaumatin-like proteins, chitinases) and yeast peptides influencing stability and sensory properties, while Botrytis cinerea infection significantly alters this balance by degrading PR proteins and introducing fungal enzymes. Altogether, the Vitis proteome emerges as a dynamic, multifunctional system crucial for understanding plant adaptation, enological quality, and biomarker discovery. Full article
(This article belongs to the Special Issue Omics in Plant Development and Stress Responses)
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