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From Plant Genomics Investigations to Plant Biotechnology Exploitation

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 March 2026 | Viewed by 505

Special Issue Editor

Special Issue Information

Dear Colleagues,

Advances in NGS technologies and other disciplines such as proteomics and metabolomics have led to the rise of molecular-based information. Computational algorithms for the efficient storage, management, and analysis of biological data have become crucial to plant sciences. The availability of many plant genome sequences and the understanding of their structure and functioning have enabled the development of methods to accelerate their modification. Plant genomics provides researchers with the main tools to pursue this goal. The use of basic scientific information to benefit an innovative process concerns the translation of science into technology. The aim of this Special Issue is to highlight recent advances in this topic through original research and scientific opinion articles. The Special Issue is dedicated to authors who have devoted their research to different aspects of applied genomics and biotechnology, illustrating their potential links. Multidisciplinary approaches capable of describing the path of discoveries are welcome. Researchers are invited to contribute to this Special Issue with original research results and review and perspective articles.

Dr. Maria R. Ercolano
Guest Editor

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Keywords

  • sequencing
  • plant genomes
  • biotechnological applications
  • translational genomics
  • new discoveries

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Published Papers (1 paper)

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Research

24 pages, 4065 KB  
Article
AI-Integrated Omics Analysis Reveals Cultivar-Specific Resistance Mechanisms to Powdery Mildew in Cucurbita pepo
by Rita Dublino, Daniela D’Esposito, Anna Guadagno, Claudio Capuozzo, Paola Crinò, Gelsomina Formisano and Maria Raffaella Ercolano
Int. J. Mol. Sci. 2025, 26(23), 11488; https://doi.org/10.3390/ijms262311488 - 27 Nov 2025
Viewed by 206
Abstract
Powdery mildew represents one of the most significant challenges for cucurbit crops. In recent decades, progress has been made in identifying resistance sources that improve yield and quality while reducing fungicide use. This study explored the molecular mechanisms underlying cucurbit responses to powdery [...] Read more.
Powdery mildew represents one of the most significant challenges for cucurbit crops. In recent decades, progress has been made in identifying resistance sources that improve yield and quality while reducing fungicide use. This study explored the molecular mechanisms underlying cucurbit responses to powdery mildew through comparative RNA-seq of two contrasting Cucurbita pepo cultivars: the partially resistant 968Rb and the susceptible True French. Differential expression analysis between inoculated and non-inoculated conditions identified 398 DEGs in 968Rb and 1129 in True French. In 968Rb, a stronger defense response emerged with cell wall reinforcement and upregulation of fructose-1,6-biphosphate aldolase genes, while True French showed activation of chitinase genes. Machine learning models, including Random Forest and K-means, identified expression features and gene modules linked to resistance. By combining conventional and Artificial Intelligence-based analyses, we identified a putative adaptive genetic variation, supported by a higher single nucleotide polymorphism density within expression clusters enriched for upregulated genes in the partial resistant cultivar 968Rb. The integration of Artificial Intelligence tools in our pipeline facilitated the understanding of the genetic basis of Cucurbita pepo resistance to Podosphaera xanthii, highlighting the transcriptional modules and variant patterns associated with resistance traits, and providing a scalable framework for future applications in crop improvement. Full article
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