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Genetic Dissection of Plant Responses to Biotic and Abiotic Stresses:...
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Genetic Dissection of Plant Responses to Biotic and Abiotic Stresses: From Gene Discovery to Functional Mechanisms

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 15 December 2026 | Viewed by 1827

Editor

Prof. Dr. Wangsheng Zhu

E-Mail Website
Guest Editor
College of Plant Protection, China Agricultural University, Beijing 100107, China
Interests: plant disease resistance; plant immunity; molecular genetics

Special Issue Information

Dear Colleague,

Plants are constantly exposed to a wide range of biotic and abiotic stresses, including pathogen infection, mycotoxin contamination, drought, salinity and temperature extremes. Understanding the genetic and molecular mechanisms underlying plant responses to these stresses is essential for improving crop resilience, productivity and food safety.

Recent advances in high-throughput genomics, such as genome-wide association studies (GWAS), transcriptomics and gene editing technologies, have greatly accelerated the identification and functional characterization of stress-responsive genes. In parallel, increasing attention has been paid to the molecular interplay between plants and their interacting organisms, including the identification of pathogen-derived effectors and their corresponding plant targets.

This Special Issue aims to provide a comprehensive overview of recent progress in plant stress biology, with particular focus on gene discovery, functional validation and mechanistic insights. We welcome original research articles and reviews that address, but are not limited to, the following topics:

  1. Identification of genes involved in plant resistance to biotic and abiotic stresses using GWAS, QTL mapping and multi-omics approaches.
  2. Functional characterization of stress-responsive genes, including transcription factors, signaling components and metabolic regulators.
  3. Genetic and molecular mechanisms underlying plant–pathogen interactions, including host plant resistance genes and susceptibility genes.
  4. Genetic basis of plant responses to mycotoxins and other phytotoxic compounds.
  5. Gene regulatory networks and signaling pathways involved in plant responses to biotic and abiotic stresses.
  6. Comparative genomics and evolutionary analysis of stress-related genes across plant species.
  7. Translational genetics for crop improvement, including the utilization of resistance genes in breeding programs.

By integrating genetic, molecular and physiological perspectives, this Special Issue seeks to advance our understanding of how plants perceive and respond to environmental challenges and to facilitate the development of stress-resilient crops.

Prof. Dr. Wangsheng Zhu
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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly 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 2600 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

  • GWAS
  • genetic variation
  • gene identification
  • stress-responsive genes
  • plant–pathogen interaction

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Published Papers (3 papers)

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Research

17 pages, 3399 KB  
Article
Pan-NLRome Analysis of Cultivated Tomato and Wild Solanum Relatives Reveals an Open Immune Repertoire Dominated by Spatially Dispersed Homologs
by Shibo Meng, Jiajun Zhu, Enmei Hu, Jia Liu, Yuan Cheng, Meiying Ruan, Chenxu Liu, Qingjing Ye, Rongqing Wang, Zhuping Yao, Zhimiao Li, Guozhi Zhou, Hongjian Wan and Yougen Chen
Genes 2026, 17(8), 864; https://doi.org/10.3390/genes17080864 - 24 Jul 2026
Viewed by 377
Abstract
Background/Objectives: Nucleotide-binding leucine-rich repeat (NLR) proteins are major intracellular immune receptors involved in effector-triggered immunity. However, the evolutionary diversity and genomic organization of NLR repertoires remain incompletely characterized in Solanaceae crops and their wild relatives. This study aimed to investigate the pan-NLRome landscape [...] Read more.
Background/Objectives: Nucleotide-binding leucine-rich repeat (NLR) proteins are major intracellular immune receptors involved in effector-triggered immunity. However, the evolutionary diversity and genomic organization of NLR repertoires remain incompletely characterized in Solanaceae crops and their wild relatives. This study aimed to investigate the pan-NLRome landscape and evolutionary patterns of tomato and related species. Methods: A comparative pan-NLRome analysis was performed across five angiosperms, including cultivated tomato (Solanum lycopersicum) and four related species (Solanum chilense, Solanum lycopersicoides, Solanum pimpinellifolium, and Arabidopsis thaliana). NLR genes were identified using an integrated HMMER- and BLASTp-based pipeline, followed by chromosome anchoring, orthogroup (OG) classification, phylogenetic analysis, spatial organization analysis, and evaluation of associations with long terminal repeat (LTR) retrotransposons. Results: A total of 1566 chromosome-anchored NLR genes were assigned to 150 OGs. Core OGs represented 25.3% of total OG diversity but contained a large proportion of NLR genes. Rarefaction analysis indicated continuous accumulation of novel OGs with increasing species sampling, supporting an open pan-NLRome structure. Phylogenetic analysis identified 18 NLR subfamilies, with SF_03 and SF_01 together accounting for approximately 79% of NLR genes. Dispersed homologs represented the predominant spatial arrangement pattern, accounting for 85.1% of NLR gene pairs across Solanaceae species. Conclusions: This study provides a comparative genomic framework for understanding NLR diversity and evolution in tomato and related Solanum species, highlighting the dynamic expansion and spatial organization of plant immune receptor repertoires and providing valuable resources for resistance gene discovery. Full article
(This article belongs to the Special Issue Genetic Dissection of Plant Responses to Biotic and Abiotic Stresses: From Gene Discovery to Functional Mechanisms)
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18 pages, 37313 KB  
Article
Integrated Transcriptome and Metabolome Analysis Elucidates the Regulatory Networks of Salt Stress Response During Cotton Seed Germination
by Yutao Guo, Li Tian, Shaoyu Cheng, Xiang Ren and Xianliang Zhang
Genes 2026, 17(7), 761; https://doi.org/10.3390/genes17070761 - 30 Jun 2026
Viewed by 440
Abstract
Background/Objectives: Soil salinization constitutes a critical threat to global agriculture, with cotton (Gossypium spp.) being highly susceptible. This abiotic stress most severely impacts cotton during the early sowing and seedling stages, compromising stand establishment and early growth. Manifestations of this stress include [...] Read more.
Background/Objectives: Soil salinization constitutes a critical threat to global agriculture, with cotton (Gossypium spp.) being highly susceptible. This abiotic stress most severely impacts cotton during the early sowing and seedling stages, compromising stand establishment and early growth. Manifestations of this stress include reduced germination rates, uneven emergence, stunted seedlings, and, ultimately, diminished boll set and fiber yield. Methods: To investigate the molecular basis of salt tolerance in cotton seed germination, we performed integrated transcriptomic and metabolomic profiling of Gossypium hirsutum cv. ST022-1056m5 under 150 mM NaCl stress at 24 h, 48 h, and 72 h, finding that salt stress significantly inhibited germination. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were identified, followed by functional enrichment and Weighted Gene Co-expression Network Analysis (WGCNA) to construct regulatory networks. Results: Transcriptomics revealed stage-specific differentially expressed genes, with predominant downregulation and enrichment in catalytic/transporter activities. Metabolomics showed distinct reprogramming, with 210 shared differentially accumulated metabolites enriched in lipids, organic acids, terpenoids, and phenolic acids. KEGG analysis highlighted time-dependent pathway shifts: sucrose metabolism and MAPK signaling at 24 h, photosynthesis at 48 h, and cuticular lipid biosynthesis at 72 h. Weighted Gene Co-expression Network Analysis (WGCNA) identified stage-associated modules and hub genes (GH_A02G0892, GH_A08G2853), and multi-omics integration indicated the strongest transcript–metabolite coordination at 24 h. Conclusion: Our study reveals dynamic molecular reprogramming underpinning stage-specific salt adaptation in germinating cotton seeds. These identified DEGs, DAMs, and hub genes represent promising candidate targets for molecular breeding and offer a crucial genetic basis for improving salt tolerance in cotton. Full article
(This article belongs to the Special Issue Genetic Dissection of Plant Responses to Biotic and Abiotic Stresses: From Gene Discovery to Functional Mechanisms)
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15 pages, 3442 KB  
Article
GWA Study Identifies Two Positive Regulators of Mycotoxin Fumonisin B1 Tolerance in Arabidopsis
by Yaxin Guan, Houpeng Wu, Zhiqing Wang, Chuang Liu and Wangsheng Zhu
Genes 2026, 17(3), 348; https://doi.org/10.3390/genes17030348 - 21 Mar 2026
Viewed by 554
Abstract
Background: Fumonisin B1 (FB1) is a toxic secondary metabolite produced by Fusarium species that commonly contaminates cereal crops, posing serious threats to crop productivity and food safety. In plants, FB1 inhibits ceramide synthase, disrupts sphingolipid metabolism, and induces growth inhibition and programmed cell [...] Read more.
Background: Fumonisin B1 (FB1) is a toxic secondary metabolite produced by Fusarium species that commonly contaminates cereal crops, posing serious threats to crop productivity and food safety. In plants, FB1 inhibits ceramide synthase, disrupts sphingolipid metabolism, and induces growth inhibition and programmed cell death. Despite the agricultural importance of fumonisin contamination, genetic strategies to enhance FB1 tolerance or detoxification capacity in crops remain limited, largely due to an incomplete understanding of the underlying genetic determinants. Methods: To identify genetic determinants associated with FB1 tolerance, we exploited natural variation in Arabidopsis thaliana and conducted a genome-wide association study (GWAS). Candidate genes were further examined using gene expression analyses and functional characterization of overexpression and SALK mutant lines. Results: GWAS revealed a significant association locus on chromosome 1 linked to FB1 tolerance. Two adjacent genes within this locus, AT1G14750 and AT1G14755, were identified as positive regulators of FB1 tolerance. Both genes were rapidly induced upon FB1 exposure. Functional analyses demonstrated that overexpression of either gene significantly enhanced tolerance to FB1-induced damage, whereas SALK mutant lines displayed increased sensitivity, manifested by enhanced growth inhibition and necrosis. Conclusions: Our study identifies AT1G14750 and AT1G14755 as previously uncharacterized components of FB1 tolerance in Arabidopsis. These findings provide new insights into the genetic architecture of plant response to mycotoxin stress and establish a foundation for further studies on the molecular mechanisms underlying FB1 tolerance. Full article
(This article belongs to the Special Issue Genetic Dissection of Plant Responses to Biotic and Abiotic Stresses: From Gene Discovery to Functional Mechanisms)
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