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Agronomy
Special Issues
Interaction Mechanisms Between Crops and Pathogens
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Interaction Mechanisms Between Crops and Pathogens

A Special Issue of Agronomy (ISSN 2073-4395) belonging to the section "Pest and Disease Management".

Deadline for manuscript submissions: closed (15 July 2026) | Viewed by 5211

Editors

Prof. Dr. Guodong Lu

E-Mail Website
Guest Editor
College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
Interests: molecular plant pathology and fungal genetics; molecular interaction between rice and Magnaporthe oryzae
Special Issues, Collections and Topics in MDPI journals
Dr. Yingzi Yun

E-Mail Website
Guest Editor
College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
Interests: fungal pathogen; pathogenesis; genomics; plant-pathogen interactions; plant disease control
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The interaction between crops and pathogens is a critical area of research with significant implications for global food security and agricultural sustainability. Pathogens, including fungi, bacteria, and viruses, utilize sophisticated strategies to infect crops, leading to devastating diseases and substantial yield losses. Understanding the molecular and cellular mechanisms underlying these interactions is essential for developing effective disease management strategies. Recent advancements in genomics, proteomics, and biotechnology have provided innovative insights into the complex interplay between crops and pathogens, including pathogen virulence factors, host immune responses, and the role of environmental factors. This Special Issue, titled "Interaction Mechanisms Between Crops and Pathogens", aims to highlight cutting-edge research and reviews that explore the molecular basis of crop–pathogen interactions, innovative diagnostic tools, and sustainable approaches to disease control. We welcome original research and review articles focused on molecular and genomic analyses of model plant–pathogen interactions or interactions between crops and pathogens that cause significant damage.

Prof. Dr. Guodong Lu
Dr. Yingzi Yun
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. Agronomy 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 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

  • crop–pathogen interactions
  • molecular mechanisms
  • pathogen virulence
  • plant immunity
  • disease management strategies

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Published Papers (5 papers)

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Research

18 pages, 22537 KB  
Article
Bacillus velezensis BV3 Suppresses Leaf Spot Pathogens via Two Antifungal Metabolites and Promotes Maize Growth
by Mengjing Wu, Yuanlin Qi, Linlin Song, Peng Huang, Jie Zhang, Deyi Yu, Zhaohua Zeng and Jin-Ai Yao
Agronomy 2026, 16(13), 1280; https://doi.org/10.3390/agronomy16131280 - 2 Jul 2026
Viewed by 362
Abstract
Southern corn leaf blight (SCLB), caused by Bipolaris maydis, poses a serious threat to maize production worldwide. In our previous study, Bacillus velezensis BV3 was isolated and demonstrated strong antagonistic activity against maize leaf spot pathogens and effective disease control in greenhouse [...] Read more.
Southern corn leaf blight (SCLB), caused by Bipolaris maydis, poses a serious threat to maize production worldwide. In our previous study, Bacillus velezensis BV3 was isolated and demonstrated strong antagonistic activity against maize leaf spot pathogens and effective disease control in greenhouse experiments. In this study, we evaluated the plant growth-promoting effects of BV3 on two maize cultivars through root application in pot experiments, and investigated the underlying molecular mechanisms using transcriptomic and metabolomic analyses. Inoculation with BV3 significantly promoted maize growth. Moreover, BV3 treatment induced extensive transcriptional and metabolic reprogramming in maize. Transcriptomic analysis identified numerous differentially expressed genes (DEGs) mainly enriched in plant–pathogen interaction, plant hormone signal transduction, MAPK signaling pathway, and phenylpropanoid biosynthesis pathways. Metabolomic analysis revealed substantial changes in metabolite accumulation, particularly in lipids, amino acids, sugars, organic acids, and polyphenols, with enriched pathways including secondary metabolite biosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis. LC/MS and GC/MS analyses further revealed that BV3 produced diverse bioactive compounds. 2,4-DTBP and surfactin exhibited strong antifungal activities, particularly against B. maydis and Exserohilum turcicum. Overall, Bacillus sp. BV3 exhibits strong biocontrol efficacy against maize leaf spot pathogens and significant plant growth-promoting activity, highlighting its potential as an eco-friendly biocontrol agent for the management of southern corn leaf blight. Full article
(This article belongs to the Special Issue Interaction Mechanisms Between Crops and Pathogens)
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21 pages, 1386 KB  
Article
The Biocontrol Effect and Induced Disease Resistance Mechanism of Bacillus velezensis FJ17-4 on Cucumber Fusarium Wilt
by Chengzhong Lan, Lin Gan, Yuli Dai, Xiaofei Liu, Xiujuan Yang, Zhenhua Lei and Hongchun Ruan
Agronomy 2026, 16(11), 1028; https://doi.org/10.3390/agronomy16111028 - 22 May 2026
Viewed by 592
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum Owen (FOC) is a major disease affecting cucumber production. Developing environmentally friendly prevention and control strategies is essential for managing cucumber Fusarium wilt (CFW). Bacillus velezensis is a beneficial microorganism with biocontrol potential against [...] Read more.
Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum Owen (FOC) is a major disease affecting cucumber production. Developing environmentally friendly prevention and control strategies is essential for managing cucumber Fusarium wilt (CFW). Bacillus velezensis is a beneficial microorganism with biocontrol potential against plant diseases. To investigate the biocontrol efficacy and induced disease resistance mechanism of B. velezensis FJ17-4 against CFW, the biocontrol effect of FJ17-4 on CFW was determined through indoor pot cultivation experiments, and the transcriptome of cucumber root samples treated with FJ17-4 was sequenced and analyzed by RNA-Seq technology. The results showed that CFW incidence was significantly reduced after FJ17-4 treatment, with 68.75% control efficacy, higher than that of Kasugamycin. A total of 1041 differentially expressed genes (DEGs) were induced, including 477 upregulated and 564 downregulated genes. DEGs associated with plant–pathogen interaction pathways (such as carbon metabolism, phenylpropanoid biosynthesis and amino acid biosynthesis), calcium (Ca2+) signaling pathway, and plant hormone signaling pathways [such as salicylic acid (SA), ethylene (ET), and jasmonic acid (JA)] were induced. These responses activated the disease resistance system of cucumber against CFW. Quantitative RT-PCR validation of 10 annotated DEGs confirmed consistent expression trends with the transcriptomic data. The results indicate that FJ17-4-induced disease resistance involves multiple genes and coordinated regulation of metabolisms, with hormone-mediated defense signaling pathways playing important roles. The transcriptome sequencing data provides a scientific basis for exploring the induced disease resistance mechanism of FJ17-4 and developing environmentally friendly biocontrol strategies. Full article
(This article belongs to the Special Issue Interaction Mechanisms Between Crops and Pathogens)
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21 pages, 2345 KB  
Article
Effects of Root Exudates on Seed Germination and Seedling Growth of Wolfberry (Lycium barbarum L.) and the Development of Root Rot Diseases
by Xiaoying Li, Lizhen Zhu, Jun He, Xiongxiong Nan, Fang Wang, Yali Wang, Hao Wang, Yu Li, Xinru He, Yuchao Chen and Ken Qin
Agronomy 2025, 15(12), 2821; https://doi.org/10.3390/agronomy15122821 - 8 Dec 2025
Viewed by 1001
Abstract
Root exudates play a critical role in enabling plants to respond to environmental stresses and mediate information exchange within the rhizosphere. These compounds regulate plant–rhizosphere interactions and significantly influence the structural and functional properties of the rhizosphere micro-ecosystem. Under continuous cropping systems, allelochemicals [...] Read more.
Root exudates play a critical role in enabling plants to respond to environmental stresses and mediate information exchange within the rhizosphere. These compounds regulate plant–rhizosphere interactions and significantly influence the structural and functional properties of the rhizosphere micro-ecosystem. Under continuous cropping systems, allelochemicals derived from root exudates progressively accumulate in the root zone, thereby contributing to the development of continuous cropping obstacles. In this study, root exudates were collected from wolfberry (Lycium barbarum L.) and four forages under controlled conditions to test their effects on seed germination and seedling growth in mangold (Betu vulgaris L.) and wolfberry, as well as on the root rot pathogen. Our research shows that forage root exudates could promote wolfberry seedling growth. White clover (Trifolium repens L.) and alfalfa (Medicago sativa L.), especially, could have their growth increased by up to 61% and 90% (p < 0.05). Wolfberry root exudates could promote the seed germination and seedling growth of white clover and mangold, the seed germination of Ryegrass (Lolium perenne L.), and the seedling growth of alfalfa. In addition, mangold root rots were identified as Molds, Aspergillus niger, and Fusarium solani and wolfberry root rots were Mucor cirrus, Rhizopus, Fusarium oxysporum, and Fusarium solani. What is more, wolfberry root exudates could promote Fusarium plaque expansion and mycelial growth. Ryegrass inhibited the growth of Mucor, Fusarium putrum, and oxysporum, and alfalfa and white clover promoted the plaque expansion of Rhizopus, Aspergillus niger, and Fusarium fulcrum, but inhibited the mycelial growth of related pathogens; mangold root exudates could inhibit wolfberry root rot, which affects interspecific relationships. This study provides robust technical support for elucidating interspecific relationships and promoting the development and application of the wolfberry-forage intercropping system. Full article
(This article belongs to the Special Issue Interaction Mechanisms Between Crops and Pathogens)
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17 pages, 1932 KB  
Article
A Mycorrhiza-Associated Receptor-like Kinase Regulates Disease Resistance in Rice
by Zichao Zheng, Ke Zou, Guodong Lu, Zonghua Wang, Haitao Cui and Airong Wang
Agronomy 2025, 15(10), 2298; https://doi.org/10.3390/agronomy15102298 - 28 Sep 2025
Cited by 1 | Viewed by 1422
Abstract
Most terrestrial plants establish symbiotic relationships with microorganisms to acquire nutrients and simultaneously restrict pathogen infection. In rice, the receptor-like kinase OsARK1 is essential for the colonization and development of arbuscular mycorrhizal (AM) fungi. However, whether OsARK1 participates in plant–pathogen interactions remain unknown. [...] Read more.
Most terrestrial plants establish symbiotic relationships with microorganisms to acquire nutrients and simultaneously restrict pathogen infection. In rice, the receptor-like kinase OsARK1 is essential for the colonization and development of arbuscular mycorrhizal (AM) fungi. However, whether OsARK1 participates in plant–pathogen interactions remain unknown. Here, we demonstrate that OsARK1 is involved in the transcriptional reprogramming of immune defense-related genes prior to and following AM colonization. Mutation of OsARK1 resulted in increased susceptibility to Magnaporthe oryzae (blast fungus) and Xanthomonas oryzae (bacterial blight). Transcriptomic profiling during blast infection demonstrated OsARK1 coordinates early immune responses; particularly, the upregulation of genes encoding lectin receptor-like kinases (LecRLKs), nucleotide-binding leucine-rich repeat (NLR) immune receptors and secondary metabolism-related genes was significantly impaired in Osark1 mutant. Collectively, OsARK1 acts as a positive regulator of rice immunity against pathogens while fine-tuning defense suppression during beneficial AM symbiosis. Full article
(This article belongs to the Special Issue Interaction Mechanisms Between Crops and Pathogens)
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15 pages, 4358 KB  
Article
Streptomyces vinaceus Mediating the Mechanism of Chinese Orchid Stomatal Closure to Enhance Resistance to Anthracnose
by Jinai Yao, Peng Huang, Jie Zhang, Xiangyu Hou and Deyi Yu
Agronomy 2025, 15(6), 1282; https://doi.org/10.3390/agronomy15061282 - 23 May 2025
Cited by 1 | Viewed by 1179
Abstract
Streptomyces vinaceus strain SVFJ-07 is a biocontrol bacterium employed to control anthracnose disease caused by Colletotrichum gloeosporioides in Chinese orchids. This study investigated the mechanism of strain SVFJ-07-induced stomatal immunity-related closure in preventing the infection of anthracnose disease. After the foliar application of [...] Read more.
Streptomyces vinaceus strain SVFJ-07 is a biocontrol bacterium employed to control anthracnose disease caused by Colletotrichum gloeosporioides in Chinese orchids. This study investigated the mechanism of strain SVFJ-07-induced stomatal immunity-related closure in preventing the infection of anthracnose disease. After the foliar application of strain SVFJ-07, we analyzed the differential patterns of stomatal opening in Chinese orchids and measured the hormone levels of abscisic acid (ABA) and salicylic acid (SA). RNA sequencing (RNA-seq) was utilized to examine the differential expression of genes involved in SA and ABA signal transduction and disease resistance genes, which were induced by strain SVFJ-07. The results demonstrated that strain SVFJ-07 inhibited the infection of pathogens by inducing stomatal closure. Compared with the control group, the foliar application of strain SVFJ-07 significantly reduced stomatal length, width, and aperture. Furthermore, orchid plants treated with strain SVFJ-07 and infected with C. gloeosporioides exhibited elevated levels of endogenous ABA and SA, indicating that strain SVFJ-07 enhanced stomatal immunity and disease resistance in these plants. The transcriptome analysis revealed the upregulation of genes associated with stomatal immunity, particularly those involved in plant–pathogen interactions, peroxisome metabolism, plant hormone signaling, and mitogen-activated protein kinase (MAPK) signaling pathways. These findings confirmed that the induction of SVFJ-07 promoted stomatal closure to resist the infection of C. gloeosporioides and induced complex transcriptome-wide changes. Further investigation of the differentially expressed genes enhanced our understanding of the resistance mechanisms induced by S. vinaceus strain SVFJ-07. Full article
(This article belongs to the Special Issue Interaction Mechanisms Between Crops and Pathogens)
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