Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
6.5
4.0
Journals
Plants
Special Issues
Molecular Biology and Genomics of Plant-Pathogen Interactions
share announcement

Molecular Biology and Genomics of Plant-Pathogen Interactions

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (28 February 2025) | Viewed by 10192

Special Issue Editor

Dr. Tika Adhikari

E-Mail Website
Guest Editor
Department of Entomology and Plant Pathology, North Carolina State University, 1575 Varsity Drive, VRB, Module # 6, Raleigh, NC 27695, USA
Interests: rice, wheat, strawberry and tomato diseases; integrated disease management; plant-pathogen interactions, genetic mapping, and GWAS; RNA-seq analysis; genotyping-by-sequencing, and plant microbiomes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant pathogens are a major problem for both natural and agricultural systems, resulting in significant economic losses. These pathogens primarily infect plants by recognizing and binding to pathogen receptors on plant cell membranes. Despite this, plants have developed complex defense mechanisms, known as plant immunity, to protect against pathogens such as bacteria, fungi and nematodes. This innate plant immunity is based on identifying pathogen-associated molecular patterns (PAMPs), which trigger the plant's basal immune responses. These responses include rapid physiological changes such as calcium uptake and the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS). These changes then induce the production of secondary metabolites, including hormones such as salicylic acid (SA), jasmonic acid (JA), ethylene (ET), abscisic acid (ABA) and pathogenesis-related (PR) proteins. When triggered by PAMPs, the response is relatively small but effective against many pathogens.

 In contrast, effector-triggered immunity (ETI) is highly specific and is activated when plants recognize pathogen effectors. This response is much stronger and is often accompanied by a hypersensitive response (HR), leading to cell death at the site of attempted host colonization. Different trophic pathogens use different strategies to attack plant hosts, with phytopathogenic viruses invading plant cells and multiplying in their cytoplasm as biotrophic pathogens.

Plants have evolved intracellular receptors called nucleotide-binding leucine-rich repeats (NLRs) to detect these cytoplasmic effectors and activate effector-triggered immunity. The interaction between these effectors and the plant immune network determines the outcome of plant–pathogen interactions. Understanding how pathogens adopt appropriate adaptive mechanisms during plant infection and exploiting the diversity of plant process mechanisms to control resistance/susceptibility to plant diseases will help protect natural and agroforestry ecosystems. This Special Issue aims to collect fascinating contributions that elucidate the complex interactions between plants and pathogens from a molecular biology and genomics perspective.

Dr. Tika Adhikari
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 100 words) can be sent to the Editorial Office for announcement on this website.

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. 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–pathogen interactions
  • effectors
  • genomics study
  • disease resistance genes
  • molecular basis
  • immunity network
  • genome‐scale network
  • pathogenomics
  • CRISPR-Cas9
  • OMICS

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

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

Published Papers (8 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

17 pages, 3480 KiB  
Article
Identification of a Papain-like Cysteine Protease Functioning as an Avirulence Factor in Striga–Cowpea Interactions
by Danhua Zhang and Michael P. Timko
Plants 2025, 14(10), 1427; https://doi.org/10.3390/plants14101427 - 9 May 2025
Viewed by 214
Abstract
While most cowpea cultivars are susceptible to parasitism by the root parasitic weed Striga gesnerioides (Willd.) Vatke, cultivar B301 is resistant to all Striga races except for SG4z. Resistance to Striga parasitism is manifested by the elicitation of a hypersensitive response (HR) at [...] Read more.
While most cowpea cultivars are susceptible to parasitism by the root parasitic weed Striga gesnerioides (Willd.) Vatke, cultivar B301 is resistant to all Striga races except for SG4z. Resistance to Striga parasitism is manifested by the elicitation of a hypersensitive response (HR) at the site of parasite attachment on the host root followed by rapid death of the attached parasite. We isolated a papain-like cysteine protease (PLCP) designated SGCP1 that is highly expressed in the haustoria of S. gesnerioides race SG3 at the time of parasite attachment to the host root. SGCP1 contains an apoplast-targeting signal peptide, a Cathepsin pro-peptide inhibitory domain, a papain family cysteine protease domain, and a granulin domain. Full-length SGCP1 and a variant lacking the signal peptide (SGCP∆SP) were expressed in the roots of composite B301 plants. Expression of SGCP1 and SGCP∆SP resulted in activation of host innate immune responses exemplified by increased frequency of HR and decreased levels of parasite cotyledon expansion (CE), indicative of successful host parasitism, in transgenic compared to wild-type B301 roots parasitized by SG4z. These data indicate that SGCP1 functions as an avirulence factor capable of activating host innate immunity and furthers our understanding of how compatible and incompatible host–parasite interactions are controlled. Full article
(This article belongs to the Special Issue Molecular Biology and Genomics of Plant-Pathogen Interactions)
►▼ Show Figures

Figure 1

23 pages, 2698 KiB  
Article
Roles of WRKY Transcription Factors in Response to Sri Lankan Cassava Mosaic Virus Infection in Susceptible and Tolerant Cassava Cultivars
by Somruthai Chaowongdee, Nattachai Vannatim, Srihunsa Malichan, Nattakorn Kuncharoen, Pumipat Tongyoo and Wanwisa Siriwan
Plants 2025, 14(8), 1159; https://doi.org/10.3390/plants14081159 - 8 Apr 2025
Viewed by 404
Abstract
Cassava mosaic disease (CMD) is caused by viruses such as Sri Lankan cassava mosaic virus (SLCMV). It poses a significant threat to the cassava (Manihot esculenta) yield in Southeast Asia. Here, we investigated the expression of WRKY transcription factors (TFs) in [...] Read more.
Cassava mosaic disease (CMD) is caused by viruses such as Sri Lankan cassava mosaic virus (SLCMV). It poses a significant threat to the cassava (Manihot esculenta) yield in Southeast Asia. Here, we investigated the expression of WRKY transcription factors (TFs) in SLCMV-infected cassava cultivars KU 50 (tolerant) and R 11 (susceptible) at 21, 32, and 67 days post-inoculation (dpi), representing the early, middle/recovery, and late infection stages, respectively. The 34 identified WRKYs were classified into the following six groups based on the functions of their homologs in the model plant Arabidopsis thaliana (AtWRKYs): plant defense; plant development; hormone signaling (abscisic, salicylic, and jasmonic acid); reactive oxygen species production; basal immune mechanisms; and other related hormones, metabolites, and abiotic stress responses. Regarding the protein interactions of the identified WRKYs, based on the interactions of their homologs (AtWRKYs), WRKYs increased reactive oxygen species production, leading to salicylic acid accumulation and systemic acquired resistance (SAR) against SLCMV. Additionally, some WRKYs were involved in defense-related mitogen-activated protein kinase signaling and abiotic stress responses. Furthermore, crosstalk among WRKYs reflected the robustly restricted viral multiplication in the tolerant cultivar, contributing to CMD recovery. This study highlights the crucial roles of WRKYs in transcriptional reprogramming, innate immunity, and responses to geminivirus infections in cassava, providing valuable insights to enhance disease resistance in cassava and, potentially, other crops. Full article
(This article belongs to the Special Issue Molecular Biology and Genomics of Plant-Pathogen Interactions)
►▼ Show Figures

Figure 1

24 pages, 5908 KiB  
Article
Understanding the Impact of Salt Stress on Plant Pathogens Through Phenotypic and Transcriptomic Analysis
by Hyejung Jung, Gil Han, Duyoung Lee, Hyun-Kyoung Jung, Young-Sam Kim, Hee Jeong Kong, Young-Ok Kim, Young-Su Seo and Jungwook Park
Plants 2025, 14(1), 97; https://doi.org/10.3390/plants14010097 - 1 Jan 2025
Viewed by 988
Abstract
For plant diseases to become established, plant pathogens require not only virulence factors and susceptible hosts, but also optimal environmental conditions. The accumulation of high soil salinity can have serious impacts on agro-biological ecosystems. However, the interactions between plant pathogens and salinity have [...] Read more.
For plant diseases to become established, plant pathogens require not only virulence factors and susceptible hosts, but also optimal environmental conditions. The accumulation of high soil salinity can have serious impacts on agro-biological ecosystems. However, the interactions between plant pathogens and salinity have not been fully characterized. This study investigated the effects of salt stress on representative plant pathogens, such as Burkholderia gladioli, Burkholderia glumae, Pectobacterium carotovorum subsp. carotovorum (Pcc), Ralstonia solanacearum, and Xanthomonas oryzae pv. oryzae. Phenotypic assays revealed that B. gladioli and R. solanacearum are highly sensitive to salt stress, exhibiting significant reductions in growth, motility, and enzyme production, whereas Pcc showed notable tolerance. Pan-genome-based comparative transcriptomics identified co-downregulated patterns in B. gladioli and R. solanacearum under stress conditions, indicating the suppression of bacterial chemotaxis and type III secretion systems. Uniquely upregulated patterns in Pcc were associated with enhanced survival under high salinity, such as protein quality control, osmotic equilibrium, and iron acquisition. Additionally, the application of salt stress combined with the beneficial bacterium Chryseobacterium salivictor significantly reduced tomato wilt caused by R. solanacearum, suggesting a potential management strategy. This study underscores practical implications for effectively understanding and controlling plant pathogens under future climate changes involving salt stress. Full article
(This article belongs to the Special Issue Molecular Biology and Genomics of Plant-Pathogen Interactions)
►▼ Show Figures

Figure 1

29 pages, 3558 KiB  
Article
Genome-Wide Transcriptional Response of Avocado to Fusarium sp. Infection
by Michel Pale, Claudia-Anahí Pérez-Torres, Catalina Arenas-Huertero, Emanuel Villafán, Diana Sánchez-Rangel and Enrique Ibarra-Laclette
Plants 2024, 13(20), 2886; https://doi.org/10.3390/plants13202886 - 15 Oct 2024
Viewed by 1490
Abstract
The avocado crop is relevant for its economic importance and because of its unique evolutionary history. However, there is a lack of information regarding the molecular processes during the defense response against fungal pathogens. Therefore, using a genome-wide approach in this work, we [...] Read more.
The avocado crop is relevant for its economic importance and because of its unique evolutionary history. However, there is a lack of information regarding the molecular processes during the defense response against fungal pathogens. Therefore, using a genome-wide approach in this work, we investigated the transcriptional response of the Mexican horticultural race of avocado (Persea americana var. drymifolia), including miRNAs profile and their possible targets. For that, we established an avocado–Fusarium hydroponic pathosystem and studied the response for 21 days. To guarantee robustness in the analysis, first, we improved the avocado genome assembly available for this variety, resulting in 822.49 Mbp in length with 36,200 gene models. Then, using an RNA-seq approach, we identified 13,778 genes differentially expressed in response to the Fusarium infection. According to their expression profile across time, these genes can be clustered into six groups, each associated with specific biological processes. Regarding non-coding RNAs, 8 of the 57 mature miRNAs identified in the avocado genome are responsive to infection caused by Fusarium, and the analysis revealed a total of 569 target genes whose transcript could be post-transcriptionally regulated. This study represents the first research in avocados to comprehensively explore the role of miRNAs in orchestrating defense responses against Fusarium spp. Also, this work provides valuable data about the genes involved in the intricate response of the avocado during fungal infection. Full article
(This article belongs to the Special Issue Molecular Biology and Genomics of Plant-Pathogen Interactions)
►▼ Show Figures

Figure 1

19 pages, 3716 KiB  
Article
Dissection of Common Rust Resistance in Tropical Maize Multiparent Population through GWAS and Linkage Studies
by Linzhuo Li, Fuyan Jiang, Yaqi Bi, Xingfu Yin, Yudong Zhang, Shaoxiong Li, Xingjie Zhang, Meichen Liu, Jinfeng Li, Ranjan K. Shaw, Babar Ijaz and Xingming Fan
Plants 2024, 13(10), 1410; https://doi.org/10.3390/plants13101410 - 18 May 2024
Cited by 1 | Viewed by 1579
Abstract
Common rust (CR), caused by Puccina sorghi, is a major foliar disease in maize that leads to quality deterioration and yield losses. To dissect the genetic architecture of CR resistance in maize, this study utilized the susceptible temperate inbred line Ye107 as [...] Read more.
Common rust (CR), caused by Puccina sorghi, is a major foliar disease in maize that leads to quality deterioration and yield losses. To dissect the genetic architecture of CR resistance in maize, this study utilized the susceptible temperate inbred line Ye107 as the male parent crossed with three resistant tropical maize inbred lines (CML312, D39, and Y32) to generate 627 F7 recombinant inbred lines (RILs), with the aim of identifying maize disease-resistant loci and candidate genes for common rust. Phenotypic data showed good segregation between resistance and susceptibility, with varying degrees of resistance observed across different subpopulations. Significant genotype effects and genotype × environment interactions were observed, with heritability ranging from 85.7% to 92.2%. Linkage and genome-wide association analyses across the three environments identified 20 QTLs and 62 significant SNPs. Among these, seven major QTLs explained 66% of the phenotypic variance. Comparison with six SNPs repeatedly identified across different environments revealed overlap between qRUST3-3 and Snp-203,116,453, and Snp-204,202,469. Haplotype analysis indicated two different haplotypes for CR resistance for both the SNPs. Based on LD decay plots, three co-located candidate genes, Zm00001d043536, Zm00001d043566, and Zm00001d043569, were identified within 20 kb upstream and downstream of these two SNPs. Zm00001d043536 regulates hormone regulation, Zm00001d043566 controls stomatal opening and closure, related to trichome, and Zm00001d043569 is associated with plant disease immune responses. Additionally, we performed candidate gene screening for five additional SNPs that were repeatedly detected across different environments, resulting in the identification of five candidate genes. These findings contribute to the development of genetic resources for common rust resistance in maize breeding programs. Full article
(This article belongs to the Special Issue Molecular Biology and Genomics of Plant-Pathogen Interactions)
►▼ Show Figures

Figure 1

29 pages, 5793 KiB  
Article
Transcriptome-Wide N6-Methyladenosine (m6A) Methylation Analyses in a Compatible Wheat–Puccinia striiformis f. sp. tritici Interaction
by Elif Naz Cerav, Nan Wu and Mahinur S. Akkaya
Plants 2024, 13(7), 982; https://doi.org/10.3390/plants13070982 - 29 Mar 2024
Cited by 2 | Viewed by 2316
Abstract
N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic mRNA, tRNA, miRNA, and long non-coding RNA. It is also known for its role in plant responses to biotic and abiotic stresses. However, a comprehensive m6A transcriptome-wide map [...] Read more.
N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic mRNA, tRNA, miRNA, and long non-coding RNA. It is also known for its role in plant responses to biotic and abiotic stresses. However, a comprehensive m6A transcriptome-wide map for Puccinia striiformis f. sp. tritici (Pst) infections in wheat (Triticum aestivum) is currently unavailable. Our study is the first to profile m6A modifications in wheat infected with a virulent Pst race. Analysis of RNA-seq and MeRIP-seq data revealed that the majority of differentially expressed genes are up-regulated and hyper-methylated. Some of these genes are enriched in the plant–pathogen interaction pathway. Notably, genes related to photosynthesis showed significant down-regulation and hypo-methylation, suggesting a potential mechanism facilitating successful Pst invasion by impairing photosynthetic function. The crucial genes, epitomizing the core molecular constituents that fortify plants against pathogenic assaults, were detected with varying expression and methylation levels, together with a newly identified methylation motif. Additionally, m6A regulator genes were also influenced by m6A modification, and their expression patterns varied at different time points of post-inoculation, with lower expression at early stages of infection. This study provides insights into the role of m6A modification regulation in wheat’s response to Pst infection, establishing a foundation for understanding the potential function of m6A RNA methylation in plant resistance or susceptibility to pathogens. Full article
(This article belongs to the Special Issue Molecular Biology and Genomics of Plant-Pathogen Interactions)
►▼ Show Figures

Figure 1

12 pages, 1113 KiB  
Article
Genome-Wide Association Analysis Uncovers Genes Associated with Resistance to Head Smut Pathotype 5 in Senegalese Sorghum Accessions
by Ezekiel Ahn, Louis K. Prom, Sunchung Park, Zhenbin Hu and Clint W. Magill
Plants 2024, 13(7), 977; https://doi.org/10.3390/plants13070977 - 29 Mar 2024
Cited by 2 | Viewed by 1667
Abstract
A newly documented pathotype 5 of the soil-borne fungus Sporisorium reilianum, causing head smut in sorghum, was tested against 153 unexplored Senegalese sorghum accessions. Among the 153 sorghum accessions tested, 63 (41%) exhibited complete resistance, showing no signs of infection by the [...] Read more.
A newly documented pathotype 5 of the soil-borne fungus Sporisorium reilianum, causing head smut in sorghum, was tested against 153 unexplored Senegalese sorghum accessions. Among the 153 sorghum accessions tested, 63 (41%) exhibited complete resistance, showing no signs of infection by the fungus. The remaining 90 accessions (59%) displayed varying degrees of susceptibility. Sorghum responses against S. reilianum were explored to analyze the potential link with previously known seed morphology-related traits and new phenotype data from 59 lines for seed weight. A genome-wide association study (GWAS) screened 297,876 SNPs and identified highly significant associations (p < 1 × 10−5) with head smut resistance in sorghum. By mapping these significant SNPs to the reference genome, this study revealed 35 novel candidate defense genes potentially involved in disease resistance. Full article
(This article belongs to the Special Issue Molecular Biology and Genomics of Plant-Pathogen Interactions)
►▼ Show Figures

Figure 1

Review

Jump to: Research

36 pages, 1572 KiB  
Review
Combating Root-Knot Nematodes (Meloidogyne spp.): From Molecular Mechanisms to Resistant Crops
by Himanshu Yadav, Philip A. Roberts and Damar Lopez-Arredondo
Plants 2025, 14(9), 1321; https://doi.org/10.3390/plants14091321 - 27 Apr 2025
Viewed by 555
Abstract
Root-knot nematodes (RKNs; Meloidogyne spp.) are significant plant–parasitic nematodes that cause major yield losses worldwide. With growing awareness of the harmful effects of chemical pesticides on human health and the environment, there is an urgent need to develop alternative strategies for controlling RKN [...] Read more.
Root-knot nematodes (RKNs; Meloidogyne spp.) are significant plant–parasitic nematodes that cause major yield losses worldwide. With growing awareness of the harmful effects of chemical pesticides on human health and the environment, there is an urgent need to develop alternative strategies for controlling RKN in agricultural fields. In recent years, implementing multiple approaches based on transcriptomics, genomics, and genome engineering, including modern platforms like CRISPR/Cas9, along with traditional genetic mapping, has led to great advances in understanding the plant–RKN interactions and the underlying molecular mechanisms of plant RKN resistance. In this literature review, we synthesize the contributions of relevant studies in this field and discuss key findings. This includes, for instance, transcriptomics studies that helped expand our understanding of plant RKN-resistance mechanisms, the overexpression of plant hormone-related genes, and the silencing of susceptibility genes that lead to plant RKN resistance. This review was conducted by searching scientific sources, including PubMed and Google Scholar, for relevant publications and filtering them using keywords such as RKN–plant defense mechanisms, host–plant resistance against RKN, and genetic mapping for RKN. This knowledge can be leveraged to accelerate the development of RKN-resistant plants and substantially improve RKN management in economically important crops. Full article
(This article belongs to the Special Issue Molecular Biology and Genomics of Plant-Pathogen Interactions)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-8
Back to TopTop