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Advances in the Molecular Diagnostics of Agriculture Pathogens and Pests

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: 30 April 2024 | Viewed by 3752

Special Issue Editor

Dr. Sergei A. Subbotin

E-Mail Website
Guest Editor
California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento, CA 95832, USA
Interests: nematology; molecular systematics; phylogenetics; molecular diagnostics; phylogeography; phylogenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant pathogens and pests are a serious threat to agriculture in every country and induce the loss of billions of dollars globally on an annual basis. In order to minimize the damage done to crops during growth, these industries must develop harvest and postharvest processing techniques, as well accurate and cost-effective tools for the detection of pathogens and pests, in order to maximize productivity and ensure agricultural sustainability. Modern developments use high-throughput molecular detection strategies for the identification of these organisms. With the expansion of  molecular diagnostic approaches in recent years, there are a lot of perspectives on the development and application of molecular diagnostics in crop protection. The molecular tools used in plant disease and pest diagnossis must be more reliable, faster and cheaper. This Special Issue of IJMS invites researchers to original research articles describing recent advances in the molecular diagnostics of plant pathogenic bacteria, fungi, viruses, and nematodes, as well as agriculturally important insects and mites. Critical reviews on this topic are also welcome in this Issue.

Dr. Sergei A. Subbotin
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 pathogens
  • pests
  • high-throughput molecular detection
  • molecular diagnostics
  • plant pathogenic bacteria

Published Papers (4 papers)

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Research

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15 pages, 5013 KiB  
Article
Identification of Viruses Infecting Phalaenopsis Orchids Using Nanopore Sequencing and Development of an RT-RPA-CRISPR/Cas12a for Rapid Visual Detection of Nerine Latent Virus
by Hyo-Jeong Lee, Hae-Jun Kim, In-Sook Cho and Rae-Dong Jeong
Int. J. Mol. Sci. 2024, 25(5), 2666; https://doi.org/10.3390/ijms25052666 - 25 Feb 2024
Viewed by 736
Abstract
Phalaenopsis orchids are one of the most popular ornamental plants. More than thirty orchid viruses have been reported, and virus-infected Phalaenopsis orchids significantly lose their commercial value. Therefore, the development of improved viral disease detection methods could be useful for quality control in [...] Read more.
Phalaenopsis orchids are one of the most popular ornamental plants. More than thirty orchid viruses have been reported, and virus-infected Phalaenopsis orchids significantly lose their commercial value. Therefore, the development of improved viral disease detection methods could be useful for quality control in orchid cultivation. In this study, we first utilized the MinION, a portable sequencing device based on Oxford Nanopore Technologies (ONT) to rapidly detect plant viruses in Phalaenopsis orchids. Nanopore sequencing revealed the presence of three plant viruses in Phalaenopsis orchids: odontoglossum ringspot virus, cymbidium mosaic virus, and nerine latent virus (NeLV). Furthermore, for the first time, we detected NeLV infection in Phalaenopsis orchids using nanopore sequencing and developed the reverse transcription–recombinase polymerase amplification (RT-RPA)-CRISPR/Cas12a method for rapid, instrument-flexible, and accurate diagnosis. The developed RT-RPA-CRISPR/Cas12a technique can confirm NeLV infection in less than 20 min and exhibits no cross-reactivity with other viruses. To determine the sensitivity of RT-RPA-CRISPR/Cas12a for NeLV, we compared it with RT-PCR using serially diluted transcripts and found a detection limit of 10 zg/μL, which is approximately 1000-fold more sensitive. Taken together, the ONT platform offers an efficient strategy for monitoring plant viral pathogens, and the RT-RPA-CRISPR/Cas12a method has great potential as a useful tool for the rapid and sensitive diagnosis of NeLV. Full article
(This article belongs to the Special Issue Advances in the Molecular Diagnostics of Agriculture Pathogens and Pests)
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14 pages, 6322 KiB  
Article
Rapid Detection of the Strawberry Foliar Nematode Aphelenchoides fragariae Using Recombinase Polymerase Amplification Assay with Lateral Flow Dipsticks
by Sergei A. Subbotin
Int. J. Mol. Sci. 2024, 25(2), 844; https://doi.org/10.3390/ijms25020844 - 10 Jan 2024
Viewed by 827
Abstract
Rapid and reliable diagnostic methods for plant-parasitic nematodes are critical for facilitating the selection of effective control measures. A diagnostic recombinase polymerase amplification (RPA) assay for Aphelenchoides fragariae using a TwistAmp® Basic Kit (TwistDx, Cambridge, UK) and AmplifyRP® Acceler8® Discovery [...] Read more.
Rapid and reliable diagnostic methods for plant-parasitic nematodes are critical for facilitating the selection of effective control measures. A diagnostic recombinase polymerase amplification (RPA) assay for Aphelenchoides fragariae using a TwistAmp® Basic Kit (TwistDx, Cambridge, UK) and AmplifyRP® Acceler8® Discovery Kit (Agdia, Elkhart, IN, USA) combined with lateral flow dipsticks (LF) has been developed. In this study, a LF-RPA assay was designed that targets the ITS rRNA gene of A. fragariae. This assay enables the specific detection of A. fragariae from crude nematode extracts without a DNA extraction step, and from DNA extracts of plant tissues infected with this nematode species. The LF-RPA assay showed reliable detection within 18–25 min with a sensitivity of 0.03 nematode per reaction tube for crude nematode extracts or 0.3 nematode per reaction tube using plant DNA extracts from 0.1 g of fresh leaves. The LF-RPA assay was developed and validated with a wide range of nematode and plant samples. Aphelenchoides fragariae was identified from seed samples in California. The LF-RPA assay has great potential for nematode diagnostics in the laboratory with minimal available equipment. Full article
(This article belongs to the Special Issue Advances in the Molecular Diagnostics of Agriculture Pathogens and Pests)
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21 pages, 4945 KiB  
Article
Integrated Transcriptome and Metabolome Dynamic Analysis of Galls Induced by the Gall Mite Aceria pallida on Lycium barbarum Reveals the Molecular Mechanism Underlying Gall Formation and Development
by Mengke Yang, Huanle Li, Haili Qiao, Kun Guo, Rong Xu, Hongshuang Wei, Jianhe Wei, Sai Liu and Changqing Xu
Int. J. Mol. Sci. 2023, 24(12), 9839; https://doi.org/10.3390/ijms24129839 - 07 Jun 2023
Cited by 1 | Viewed by 1335
Abstract
Galls have become the best model for exploring plant–gall inducer relationships, with most studies focusing on gall-inducing insects but few on gall mites. The gall mite Aceria pallida is a major pest of wolfberry, usually inducing galls on its leaves. For a better [...] Read more.
Galls have become the best model for exploring plant–gall inducer relationships, with most studies focusing on gall-inducing insects but few on gall mites. The gall mite Aceria pallida is a major pest of wolfberry, usually inducing galls on its leaves. For a better understanding of gall mite growth and development, the dynamics of the morphological and molecular characteristics and phytohormones of galls induced by A. pallida were studied by histological observation, transcriptomics and metabolomics. The galls developed from cell elongation of the epidermis and cell hyperplasia of mesophylls. The galls grew quickly, within 9 days, and the mite population increased rapidly within 18 days. The genes involved in chlorophyll biosynthesis, photosynthesis and phytohormone synthesis were significantly downregulated in galled tissues, but the genes associated with mitochondrial energy metabolism, transmembrane transport, carbohydrates and amino acid synthesis were distinctly upregulated. The levels of carbohydrates, amino acids and their derivatives, and indole-3-acetic acid (IAA) and cytokinins (CKs), were markedly enhanced in galled tissues. Interestingly, much higher contents of IAA and CKs were detected in gall mites than in plant tissues. These results suggest that galls act as nutrient sinks and favor increased accumulation of nutrients for mites, and that gall mites may contribute IAA and CKs during gall formation. Full article
(This article belongs to the Special Issue Advances in the Molecular Diagnostics of Agriculture Pathogens and Pests)
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Review

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12 pages, 1325 KiB  
Review
Isothermal Nucleic Acid Amplification-Based Lateral Flow Testing for the Detection of Plant Viruses
by Xuemei Song, Yuhao Cao and Fei Yan
Int. J. Mol. Sci. 2024, 25(8), 4237; https://doi.org/10.3390/ijms25084237 - 11 Apr 2024
Viewed by 290
Abstract
Isothermal nucleic acid amplification-based lateral flow testing (INAA-LFT) has emerged as a robust technique for on-site pathogen detection, providing a visible indication of pathogen nucleic acid amplification that rivals or even surpasses the sensitivity of real-time quantitative PCR. The isothermal nature of INAA-LFT [...] Read more.
Isothermal nucleic acid amplification-based lateral flow testing (INAA-LFT) has emerged as a robust technique for on-site pathogen detection, providing a visible indication of pathogen nucleic acid amplification that rivals or even surpasses the sensitivity of real-time quantitative PCR. The isothermal nature of INAA-LFT ensures consistent conditions for nucleic acid amplification, establishing it as a crucial technology for rapid on-site pathogen detection. However, despite its considerable promise, the widespread application of isothermal INAA amplification-based lateral flow testing faces several challenges. This review provides an overview of the INAA-LFT procedure, highlighting its advancements in detecting plant viruses. Moreover, the review underscores the imperative of addressing the existing limitations and emphasizes ongoing research efforts dedicated to enhancing the applicability and performance of this technology in the realm of rapid on-site testing. Full article
(This article belongs to the Special Issue Advances in the Molecular Diagnostics of Agriculture Pathogens and Pests)
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