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Carneiro RMDG, Souza CFB, Mattos VS, Correia VR. Molecular Techniques for Root-Knot Nematode Identification. Methods Mol Biol 2024; 2756:227-245. [PMID: 38427296 DOI: 10.1007/978-1-0716-3638-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Among plant-parasitic nematodes, root-knot nematodes (RKN), Meloidogyne spp., are the most important parasite infecting economically important crops globally and causing severe losses in crop production. The use of efficient nematode control methods against these parasites depends upon their correct detection in roots and soil samples. Currently, the use of integrated identification methods, including biochemical, molecular, and morphological-based characters, is preferred. But the techniques using morphology and phylogenetic analysis are time-consuming and not suitable for routine analysis. They have only been used for studies of cryptic species, which were identified using integrative taxonomy. Here we describe the enzymatic and molecular-based methods that have successfully been used in Brazil for more than 25 years in the Nematology Lab at Embrapa Genetic Resources and Biotechnology for routine analysis. This technique is a combination of isozyme esterase profiling and molecular markers, with the aim of having a rapid and correct diagnosis of Meloidogyne spp. populations from field and greenhouse.
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Affiliation(s)
- Regina M D G Carneiro
- Embrapa Recursos Genéticos e Biotecnologia, PqEB Parque de Estação Biológica, Brasília, DF, Brazil.
| | - Caio F B Souza
- Embrapa Recursos Genéticos e Biotecnologia, PqEB Parque de Estação Biológica, Brasília, DF, Brazil
| | - Vanessa S Mattos
- Embrapa Recursos Genéticos e Biotecnologia, PqEB Parque de Estação Biológica, Brasília, DF, Brazil
- Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
| | - Valdir R Correia
- Instituto Federal de Educação, Ciência e Tecnologia do Tocantins, Dianópolis, TO, Brazil
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Arun A, Shanthi A, Raveendran M, Seenivasan N, Pushpam R, Shandeep G. An Insight into Occurrence, Biology, and Pathogenesis of Rice Root-Knot Nematode Meloidogyne graminicola. BIOLOGY 2023; 12:987. [PMID: 37508416 PMCID: PMC10376547 DOI: 10.3390/biology12070987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 07/30/2023]
Abstract
Rice (Oryza sativa L.) is one of the most widely grown crops in the world, and is a staple food for more than half of the global total population. Root-knot nematodes (RKNs), Meloidogyne spp., and especially M. graminicola, seem to be significant rice pests, which makes them the most economically important plant-parasitic nematode in this crop. RKNs develop a feeding site in galls by causing host cells to differentiate into hypertrophied, multinucleate, metabolically active cells known as giant cells. This grazing framework gives the nematode a constant food source, permitting it to develop into a fecund female and complete its life cycle inside the host root. M. graminicola effector proteins involved in nematode parasitism, including pioneer genes, were functionally characterized in earlier studies. Molecular modelling and docking studies were performed on Meloidogyne graminicola protein targets, such as β-1,4-endoglucanase, pectate lyase, phospholipase B-like protein, and G protein-coupled receptor kinase, to understand the binding affinity of Beta-D-Galacturonic Acid, 2,6,10,15,19,23-hexamethyltetracosane, (2S)-2-amino-3-phenylpropanoic acid, and 4-O-Beta-D-Galactopyranosyl-Alpha-D-Glucopyranose against ligand molecules of rice. This study discovered important molecular aspects of plant-nematode interaction and candidate effector proteins that were regulated by M. graminicola-infected rice plants. To the best of our knowledge, this is the first study to describe M. graminicola's molecular adaptation to host parasitism.
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Affiliation(s)
- Arunachalam Arun
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
| | - Annaiyan Shanthi
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
| | - Muthurajan Raveendran
- Directorate of Research, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
| | | | - Ramamoorthy Pushpam
- Department of Rice, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
| | - Ganeshan Shandeep
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
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3
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Shift from morphological to recent advanced molecular approaches for the identification of nematodes. Genomics 2022; 114:110295. [DOI: 10.1016/j.ygeno.2022.110295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
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Koehler AK, Bell CA, Back MA, Urwin PE, Atkinson HJ. Improving a pest management tool for scenario analysis of economic populations of Globodera pallida. NEMATOLOGY 2021. [DOI: 10.1163/15685411-bja10138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Globodera pallida is the most damaging pest of potato in the UK. This work underpins enhancement of a well-established, web-based scenario analysis tool for its management by recommending additions and modifications of its required inputs and a change in the basis of yield loss estimates. The required annual decline rate of the dormant egg population is determined at the individual field sample level to help define the required rotation length by comparing the viable egg content of recovered cysts to that of newly formed cysts for the same projected area. The mean annual decline was 20.4 ± 1.4% but ranged from 4.0 to 39.7% annum−1 at the field level. Further changes were based on meta-analysis of previous field trials. Spring rainfall in the region where a field is located and cultivar tolerance influence yield loss. Tolerance has proved difficult to define for many UK potato cultivars in field trials but uncertainty can be avoided without detriment by replacing it with determinacy integers. They are already determined to support optimisation of nitrogen application rates. Multiple linear regression estimates that loss caused by pre-plant populations of up to 20 viable eggs (g soil)−1 varies from ca 0.2 to 2.0% (viable egg)−1 (g soil)−1 depending on cultivar determinacy and spring rainfall. Reliability of the outcomes from scenario analysis requires validation in field trials with population densities over which planting is advisable.
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Affiliation(s)
- Ann-Kristin Koehler
- Institute of Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, UK
| | | | - Matthew A. Back
- Crop and Environment Sciences, Harper Adams University, Newport, Shropshire, UK
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Pan F, Li F, Mao Y, Liu D, Chen A, Zhao D, Hu Y. First Detection of Ditylenchus destructor Parasitizing Maize in Northeast China. Life (Basel) 2021; 11:life11121303. [PMID: 34947834 PMCID: PMC8706602 DOI: 10.3390/life11121303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Maize is one of the most important crops in the world. Heilongjiang province has the largest maize area in China. Plant-parasitic nematodes are important agricultural pests, which cause huge economic losses every year and have attracted global attention. Potato rot nematode Ditylenchus destructor is a plant-parasitic nematode with a wide range of hosts and strong survival ability in different environments, which brings risks to agricultural production. In 2020, D. destructor was detected in seven maize fields in Heilongjiang province. Morphological identification and molecular approach were used to characterize the isolated D. destructor. The observed morphological and morphometric characteristics were highly similar and consistent with the existing description. The DNA sequencing on the D2/D3 region of the ribosomal DNA 28S and the phylogenetic analysis showed that D. destructor population obtained from maize and other isolates infesting carrot, sweet potato, and potato were in subclade I supported by a 96% bootstrap value. Additionally, the phylogenetic analysis of the ITS rRNA gene sequence further indicated that this D. destructor population from maize clustered in a clade I group and belonged to ITS rRNA haplotype C. An inoculation experiment revealed that D. destructor was pathogenic on the maize seedlings in pots and caused the disease symptoms in the stem base of maize seedlings. This is the first report of D. destructor causing stem rot of maize in Heilongjiang province, and contributes additional information on disease control and safe production of maize in the region.
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Affiliation(s)
- Fengjuan Pan
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China;
| | - Feng Li
- Syngenta (China) Investment Co., Ltd., Beijing 102206, China; (F.L.); (D.L.)
| | - Yanzhi Mao
- Heilongjiang Academy of Agricultural Sciences, Harbin 154026, China; (Y.M.); (D.Z.)
| | - Dan Liu
- Syngenta (China) Investment Co., Ltd., Beijing 102206, China; (F.L.); (D.L.)
| | - Aoshuang Chen
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150006, China;
| | - Dan Zhao
- Heilongjiang Academy of Agricultural Sciences, Harbin 154026, China; (Y.M.); (D.Z.)
| | - Yanfeng Hu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China;
- Correspondence:
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Tavoillot J, Mateille T, Ali N, Chappé AM, Martin JF. Early Detection of the Root-Knot Nematode Meloidogyne hapla Through Developing a Robust Quantitative PCR Approach Compliant with the Minimum Information for Publication of Quantitative Real-Time PCR Experiments Guidelines. PLANT DISEASE 2021; 105:2836-2843. [PMID: 33900116 DOI: 10.1094/pdis-11-20-2408-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Root-knot nematodes (RKNs) are major threats to crops through attacking the roots, which induces an abnormal development of the plant. Meloidogyne hapla is of particular concern, as it is currently expanding its distribution area and displays a wide host range. Effective plant protection against this RKN requires early detection, as even a single individual can cause severe economic losses on susceptible crops. Molecular tools are of particular value for this purpose, and among them, quantitative PCR (qPCR) presents many advantages (i.e., sensitivity, specificity, and rapidity of diagnosis at a reduced cost). Although a few studies have already been proposed for detecting M. hapla through this technique, they lack experimental details and performance testing, suffer from low taxonomic resolution, and/or require expensive hydrolysis probes. Here, we propose a qPCR detection method that uses SYBR Green with developed primers amplifying a fragment of the cytochrome oxidase I mitochondrial region. The method was developed and evaluated following the minimum information for publication of quantitative real-time PCR experiments (MIQE) guidelines to ensure its quality (i.e., sensitivity, specificity, repeatability, reproducibility, and robustness). The results demonstrate that the newly developed method fulfills its goals, as it proved specific to M. hapla and allowed for a reproductible detection level as low as 1.25 equivalent of a juvenile individual. All criteria associated with the MIQE guidelines were also met, so the method is of general use for the reliable early detection of M. hapla.
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Affiliation(s)
- Johannes Tavoillot
- Biology Center for Population Management (CBGP), Université de Montpellier, Center for International Cooperation in Agricultural Research for Development (CIRAD), National Institute for Agricultural Research (INRAE), Institut Agro, Institute of Research for Development (IRD) Montpellier, 34988 Montpellier, France
| | - Thierry Mateille
- Biology Center for Population Management (CBGP), Université de Montpellier, Center for International Cooperation in Agricultural Research for Development (CIRAD), National Institute for Agricultural Research (INRAE), Institut Agro, Institute of Research for Development (IRD) Montpellier, 34988 Montpellier, France
| | - Nadine Ali
- Department of Plant Protection, Tishreen University, Tishreen, Syria
| | - Anne-Marie Chappé
- Nematology Unit, Anses, French Agency for Food, Environmental and Occupational Health and Safety/Plant Health Laboratory, 35653 Le Rheu, France
| | - Jean-François Martin
- Biology Center for Population Management (CBGP), Université de Montpellier, Center for International Cooperation in Agricultural Research for Development (CIRAD), National Institute for Agricultural Research (INRAE), Institut Agro, Institute of Research for Development (IRD) Montpellier, 34988 Montpellier, France
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Chi YK, Zhao W, Ye MD, Ali F, Wang T, Qi RD. Evaluation of Recombinase Polymerase Amplification Assay for Detecting Meloidogyne javanica. PLANT DISEASE 2020; 104:801-807. [PMID: 31944903 DOI: 10.1094/pdis-07-19-1473-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Meloidogyne javanica is one of the most widespread and economically important nematodes in many countries, including China. In this study, a recombinase polymerase amplification (RPA) assay was evaluated for the detection of M. javanica based on the sequences of a sequence-characterized amplified regions marker gene segment. The RPA assay specifically detected M. javanica from individual juvenile or adult female, M. javanica-induced galls, and nematodes in the soil samples. The detection limit of M. javanica RPA assay was 1 pg of purified genomic DNA, 0.01 adult female, or 0.1 second-stage juvenile, which was 10 times more sensitive than conventional PCR assay. Furthermore, combined with lateral flow dipstick (LFD), a visual detection method of LFD-RPA assay was developed, which is suitable for onsite surveys and routine diagnostics. Results indicate that the RPA assay is rapid, sensitive, and reliable for detection and molecular identification of M. javanica.
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Affiliation(s)
- Yuan-Kai Chi
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Wei Zhao
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Meng-di Ye
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Farman Ali
- Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan
| | - Tao Wang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ren-de Qi
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
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da Silva Mattos V, Mulet K, Cares JE, Gomes CB, Fernandez D, de Sá MFG, Carneiro RMDG, Castagnone-Sereno P. Development of Diagnostic SCAR Markers for Meloidogyne graminicola, M. oryzae, and M. salasi Associated with Irrigated Rice Fields in Americas. PLANT DISEASE 2019; 103:83-88. [PMID: 30412451 DOI: 10.1094/pdis-12-17-2015-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Root-knot nematodes (RKN) cause important production losses of rice (Oryza sativa L.) in the world. Together with Meloidogyne graminicola Golden and Birchfield 1965, M. oryzae Maas, Sanders and Dede, 1978 and M. salasi López, 1984 have been causing damages in irrigated rice fields in Central and South America. In addition, six other RKN species may occur in rice fields in other regions of the world. Correct identification of Meloidogyne spp. is difficult but essential for the management of rice RKNs. The objective of this study was to develop some species-specific molecular markers for the diagnosis of South American RKN rice-related species. Isozyme phenotypes indicated the occurrence of some RKN species in the Brazilian samples, namely M. graminicola, M. oryzae, M. javanica, and two cryptic species designated as Meloidogyne sp. 2 and Meloidogyne sp. 3. Random amplified polymorphic DNA (RAPD) analysis of 16 isolates revealed interspecific genetic polymorphism between Meloidogyne spp., but isolates belonging to the same species (i.e., sharing the same esterase phenotype) always clustered together, whatever the species considered. Specific SCAR markers of 230, 120, and 160 bp were developed for M. graminicola, M. oryzae, and M. salasi, respectively. These SCAR markers may be potential molecular tools for application in routine diagnostic procedures subject to their validation with other rice RKN field populations in the world.
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Affiliation(s)
- Vanessa da Silva Mattos
- Departamento de Fitopatologia, Universidade de Brasília, Brasília, DF 70910-900, Brazil, and Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, 70849-979 Brasília-DF, Brazil
| | | | - Juvenil Enrique Cares
- Departamento de Fitopatologia, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | | | - Diana Fernandez
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | | | - Regina M D G Carneiro
- Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, 70849-979 Brasília-DF, Brazil
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9
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Genetic diversity and phylogeny of South African Meloidogyne populations using genotyping by sequencing. Sci Rep 2018; 8:13816. [PMID: 30217984 PMCID: PMC6138707 DOI: 10.1038/s41598-018-31963-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/30/2018] [Indexed: 11/13/2022] Open
Abstract
Meloidogyne species cause great crop losses worldwide. Although genetic host plant resistance is an effective control strategy to minimize damage caused by Meloidogyne, some resistant genes are ineffective against virulent species such as Meloidogyne enterolobii. Detailed knowledge about the genetic composition of Meloidogyne species is thus essential. This study focused on genotyping-by-sequencing (GBS) and Pool-Seq to elucidate the genetic relation between South African M. enterolobii, M. incognita and M. javanica populations. Hence, 653 common single nucleotide polymorphisms (SNPs) were identified and used to compare these species at genetic level. Allele frequencies of 34 SNPs consistently differed between the three Meloidogyne species studied. Principal component and phylogenetic analyses grouped the M. enterolobii populations in one clade, showing a distant relation to the M. javanica populations. These two species also shared genetic links with the M. incognita populations studied. GBS has been used successfully in this study to identify SNPs that discriminated among the three Meloidogyne species investigated. Alleles, only occurring in the genome of M. enterolobii and located in genes involved in virulence in other animal species (e.g. a serine/threonine phosphatase and zinc finger) have also been identified, accentuating the value of GBS in future studies of this nature.
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Bell CA, Atkinson HJ, Andrade AC, Nguyen HX, Swibawa IG, Lilley CJ, McCarthy J, Urwin PE. A High-Throughput Molecular Pipeline Reveals the Diversity in Prevalence and Abundance of Pratylenchus and Meloidogyne Species in Coffee Plantations. PHYTOPATHOLOGY 2018; 108:641-650. [PMID: 29291356 DOI: 10.1094/phyto-10-17-0343-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Coffee yields are adversely affected by plant-parasitic nematodes and the pathogens are largely underreported because a simple and reliable identification method is not available. We describe a polymerase chain reaction-based approach to rapidly detect and quantify the major Pratylenchus and Meloidogyne nematode species that are capable of parasitizing coffee. The procedure was applied to soil samples obtained from a number of coffee farms in Brazil, Vietnam, and Indonesia to assess the prevalence of these species associated both with coffee (Coffea arabica and C. canephora) and its intercropped species Musa acuminata (banana) and Piper nigrum (black pepper). Pratylenchus coffeae and P. brachyurus were associated with coffee in all three countries but there were distinct profiles of Meloidogyne spp. Meloidogyne incognita, M. exigua, and M. paranaensis were identified in samples from Brazil and M. incognita and M. hapla were detected around the roots of coffee in Vietnam. No Meloidogyne spp. were detected in samples from Indonesia. There was a high abundance of Meloidogyne spp. in soil samples in which Pratylenchus spp. were low or not detected, suggesting that the success of one genus may deter another. Meloidogyne spp. in Vietnam and Pratylenchus spp. in Indonesia were more numerous around intercropped plants than in association with coffee. The data suggest a widespread but differential nematode problem associated with coffee production across the regions studied. The issue is compounded by the current choice of intercrops that support large nematode populations. Wider application of the approach would elucidate the true global scale of the nematode problem and the cost to coffee production. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
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Affiliation(s)
- Christopher A Bell
- First, second, sixth, and eighth authors: Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; third author: Embrapa Café/Inovacafé, Lavras, Brazil; fourth author: WASI, Buon Ma Thuot, Vietnam; fifth author: UNILA, Bandar Lampung, Indonesia; and seventh author: Nestle R.D. Tours, France
| | - Howard J Atkinson
- First, second, sixth, and eighth authors: Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; third author: Embrapa Café/Inovacafé, Lavras, Brazil; fourth author: WASI, Buon Ma Thuot, Vietnam; fifth author: UNILA, Bandar Lampung, Indonesia; and seventh author: Nestle R.D. Tours, France
| | - Alan C Andrade
- First, second, sixth, and eighth authors: Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; third author: Embrapa Café/Inovacafé, Lavras, Brazil; fourth author: WASI, Buon Ma Thuot, Vietnam; fifth author: UNILA, Bandar Lampung, Indonesia; and seventh author: Nestle R.D. Tours, France
| | - Hoa X Nguyen
- First, second, sixth, and eighth authors: Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; third author: Embrapa Café/Inovacafé, Lavras, Brazil; fourth author: WASI, Buon Ma Thuot, Vietnam; fifth author: UNILA, Bandar Lampung, Indonesia; and seventh author: Nestle R.D. Tours, France
| | - I Gede Swibawa
- First, second, sixth, and eighth authors: Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; third author: Embrapa Café/Inovacafé, Lavras, Brazil; fourth author: WASI, Buon Ma Thuot, Vietnam; fifth author: UNILA, Bandar Lampung, Indonesia; and seventh author: Nestle R.D. Tours, France
| | - Catherine J Lilley
- First, second, sixth, and eighth authors: Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; third author: Embrapa Café/Inovacafé, Lavras, Brazil; fourth author: WASI, Buon Ma Thuot, Vietnam; fifth author: UNILA, Bandar Lampung, Indonesia; and seventh author: Nestle R.D. Tours, France
| | - James McCarthy
- First, second, sixth, and eighth authors: Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; third author: Embrapa Café/Inovacafé, Lavras, Brazil; fourth author: WASI, Buon Ma Thuot, Vietnam; fifth author: UNILA, Bandar Lampung, Indonesia; and seventh author: Nestle R.D. Tours, France
| | - P E Urwin
- First, second, sixth, and eighth authors: Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; third author: Embrapa Café/Inovacafé, Lavras, Brazil; fourth author: WASI, Buon Ma Thuot, Vietnam; fifth author: UNILA, Bandar Lampung, Indonesia; and seventh author: Nestle R.D. Tours, France
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11
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Peng H, Long H, Huang W, Liu J, Cui J, Kong L, Hu X, Gu J, Peng D. Rapid, simple and direct detection of Meloidogyne hapla from infected root galls using loop-mediated isothermal amplification combined with FTA technology. Sci Rep 2017; 7:44853. [PMID: 28368036 PMCID: PMC5377304 DOI: 10.1038/srep44853] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/14/2017] [Indexed: 11/26/2022] Open
Abstract
The northern root-knot nematode (Meloidogyne hapla) is a damaging nematode that has caused serious economic losses worldwide. In the present study, a sensitive, simple and rapid method was developed for detection of M. hapla in infested plant roots by combining a Flinders Technology Associates (FTA) card with loop-mediated isothermal amplification (LAMP). The specific primers of LAMP were designed based on the distinction of internal transcribed spacer (ITS) sequences between M. hapla and other Meloidogyne spp. The LAMP assay can detect nematode genomic DNA at concentrations low to 1/200 000, which is 100 times more sensitive than conventional PCR. The LAMP was able to highly specifically distinguish M. hapla from other closely related nematode species. Furthermore, the advantages of the FTA-LAMP assay to detect M. hapla were demonstrated by assaying infected root galls that were artificially inoculated. In addition, M. hapla was successfully detected from six of forty-two field samples using FTA-LAMP technology. This study was the first to provide a simple diagnostic assay for M. hapla using the LAMP assay combined with FTA technology. In conclusion, the new FTA-LAMP assay has the potential for diagnosing infestation in the field and managing the pathogen M. hapla.
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Affiliation(s)
- Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haibo Long
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiangkuan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianqi Hu
- The National Engineering Research Center of Agribiodiversity Applied Technologies, Yunnan Agricultural University, Kunming 650201, China
| | - Jianfeng Gu
- Academy of Inspection and Quarantine, Ningbo, Zhejiang, 315012, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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12
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A review of methods for nematode identification. J Microbiol Methods 2016; 138:37-49. [PMID: 27262374 DOI: 10.1016/j.mimet.2016.05.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 12/15/2022]
Abstract
Nematodes are non-segmented roundworms found in soil, aquatic environment, plants, or animals. Either useful or pathogenic, they greatly influence environmental equilibrium, human and animal health, as well as plant production. Knowledge on their taxonomy and biology are key issues to answer the different challenges associated to these organisms. Nowadays, most of the nematode taxonomy remains unknown or unclear. Several approaches are available for parasite identification, from the traditional morphology-based techniques to the sophisticated high-throughput sequencing technologies. All these techniques have advantages or drawbacks depending on the sample origin and the number of nematodes to be processed. This review proposes an overview of all newly available methods available to identify known and/or unknown nematodes with a specific focus on emerging high-throughput molecular techniques.
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Janssen T, Karssen G, Verhaeven M, Coyne D, Bert W. Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution. Sci Rep 2016; 6:22591. [PMID: 26940543 PMCID: PMC4778069 DOI: 10.1038/srep22591] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/17/2016] [Indexed: 11/17/2022] Open
Abstract
The polyphagous parthenogenetic root-knot nematodes of the genus Meloidogyne are considered to be the most significant nematode pest in sub-tropical and tropical agriculture. Despite the crucial need for correct diagnosis, identification of these pathogens remains problematic. The traditionally used diagnostic strategies, including morphometrics, host-range tests, biochemical and molecular techniques, now appear to be unreliable due to the recently-suggested hybrid origin of root-knot nematodes. In order to determine a suitable barcode region for these pathogens nine quickly-evolving mitochondrial coding genes were screened. Resulting haplotype networks revealed closely related lineages indicating a recent speciation, an anthropogenic-aided distribution through agricultural practices, and evidence for reticulate evolution within M. arenaria. Nonetheless, nucleotide polymorphisms harbor enough variation to distinguish these closely-related lineages. Furthermore, completeness of lineage sorting was verified by screening 80 populations from widespread geographical origins and variable hosts. Importantly, our results indicate that mitochondrial haplotypes are strongly linked and consistent with traditional esterase isozyme patterns, suggesting that different parthenogenetic lineages can be reliably identified using mitochondrial haplotypes. The study indicates that the barcode region Nad5 can reliably identify the major lineages of tropical root-knot nematodes.
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Affiliation(s)
- Toon Janssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
- National Plant Protection Organization, Wageningen Nematode Collection, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Myrtle Verhaeven
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Danny Coyne
- International Institute of Tropical Agriculture (IITA), c/o icipe, Kasarani, P.O. Box 30772-00100, Nairobi, Kenya
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Sapkota R, Skantar AM, Nicolaisen M. A TaqMan real-time PCR assay for detection of Meloidogyne hapla in root galls and in soil. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Early detection and quantification of Meloidogyne hapla in soil is essential for effective disease management. The purpose of this study was to develop a real-time PCR assay for detection of M. hapla in soil. Primers and a TaqMan probe were designed for M. hapla detection. The assay detected M. hapla and showed no significant amplification of DNA from non-target nematodes. The assay was able to detect M. hapla in a background of plant and soil DNA. A dilution series of M. hapla eggs in soil showed a high correlation (, ) with Ct values. The assay could predict root-knot development in carrots by testing soils before planting. The assay could be useful for management decisions in carrot cultivation.
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Affiliation(s)
- Rumakanta Sapkota
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Andrea M. Skantar
- Nematology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
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Iberkleid I, Ozalvo R, Feldman L, Elbaz M, Patricia B, Horowitz SB. Responses of tomato genotypes to avirulent and Mi-virulent Meloidogyne javanica isolates occurring in Israel. PHYTOPATHOLOGY 2014; 104:484-496. [PMID: 24724816 DOI: 10.1094/phyto-07-13-0181-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The behavior of naturally virulent Meloidogyne isolates toward the tomato resistance gene Mi in major tomato-growing areas in Israel was studied for the first time. Virulence of seven selected isolates was confirmed over three successive generations on resistant (Mi-carrying) and susceptible (non-Mi-carrying) tomato cultivars. Diagnostic markers verified the predominance of Meloidogyne javanica among virulent isolates selected on resistant tomato cultivars or rootstocks. To better understand the determinants of nematode selection on Mi-carrying plants, reproduction of Mi-avirulent and virulent isolates Mjav1 and Mjv2, respectively, measured as eggs per gram of root, on non-Mi-carrying, heterozygous (Mi/mi) and homozygous (Mi/Mi) genotypes was evaluated. Although no reproduction of Mjav1 was observed on Mi/Mi genotypes, some reproduction was consistently observed on Mi/mi plants; reproduction of Mjv2 on the homozygous and heterozygous genotypes was similar to that on susceptible cultivars, suggesting a limited quantitative effect of the Mi gene. Histological examination of giant cells induced by Mi-virulent versus avirulent isolates confirmed the high virulence of Mjv2 on Mi/mi and Mi/Mi genotypes, allowing the formation of well-developed giant-cell systems despite the Mi gene. Analysis of the plant defense response in tomato Mi/Mi, Mi/mi, and mi/mi genotypes to both avirulent and virulent isolates was investigated by quantitative real-time polymerase chain reaction. Although the jasmonate (JA)-signaling pathway was clearly upregulated by avirulent and virulent isolates on the susceptible (not carrying Mi) and heterozygous (Mi/mi) plants, no change in signaling was observed in the homozygous (Mi/Mi) resistant line following incompatible interaction with the avirulent isolate. Thus, similar to infection promoted by the avirulent isolate on the susceptible genotype, the Mi-virulent isolate induced the JA-dependent pathway, which might promote tomato susceptibility during the compatible interaction with the homozygous (Mi/Mi) resistant line. These results have important consequences for the management of Mi resistance genes for ensuring sustainable tomato farming.
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Mestrović N, Plohl M, Castagnone-Sereno P. Relevance of satellite DNA genomic distribution in phylogenetic analysis: a case study with root-knot nematodes of the genus Meloidogyne. Mol Phylogenet Evol 2008; 50:204-8. [PMID: 19007896 DOI: 10.1016/j.ympev.2008.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 05/21/2008] [Accepted: 10/06/2008] [Indexed: 01/15/2023]
Affiliation(s)
- Nevenka Mestrović
- Department of Molecular Biology, Ruder Bosković Institute, Zagreb, Croatia
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François C, Kebdani N, Barker I, Tomlinson J, Boonham N, Castagnone-Sereno P. Towards specific diagnosis of plant-parasitic nematodes using DNA oligonucleotide microarray technology: a case study with the quarantine species Meloidogyne chitwoodi. Mol Cell Probes 2005; 20:64-9. [PMID: 16330184 DOI: 10.1016/j.mcp.2005.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Accepted: 09/23/2005] [Indexed: 11/30/2022]
Abstract
In order to investigate the feasibility of a microarray-based method for diagnostics of plant-parasitic nematodes, we have developed a DNA oligonucleotide microarray to detect the nematode species Meloidogyne chitwoodi, which is listed as a quarantine organism in Europe. Oligonucleotide capture probes were designed from nematode SCAR and satellite DNA sequences and spotted onto epoxy-coated glass slides. PCR products were generated using specific primers, labeled with Cyanine 3 or Cyanine 5 fluorescent dyes, and hybridized overnight to the microarray. This methodology allowed the specific detection of M. chitwoodi DNA in pure and mixed samples (i.e. when M. chitwoodi DNA was mixed with DNA from a congeneric nematode species). Simultaneous hybridization of the microarray with two amplified targets labeled with different dyes proved to be efficient, without any competition between the targets. These results illustrate a significant step forward in the development of the DNA chip technology for nematode detection, and constitute to our knowledge the first report of production and use of oligonucleotide microarrays for the detection of plant-parasitic nematodes, using the quarantine species M. chitwoodi as a test organism.
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Affiliation(s)
- Cécile François
- INRA, UMR 1064 IPMSV, BP167, 06903 Sophia Antipolis cedex, France
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Castagnone-Sereno P. Use of satellite DNA for specific diagnosis of the quarantine root-knot nematodes Meloidogyne chitwoodi and M. fallax. ACTA ACUST UNITED AC 2000. [DOI: 10.1111/j.1365-2338.2000.tb00951.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Castagnone-Sereno P, Leroy F, Bongiovanni M, Zijlstra C, Abad P. Specific Diagnosis of Two Root-Knot Nematodes, Meloidogyne chitwoodi and M. fallax, with Satellite DNA Probes. PHYTOPATHOLOGY 1999; 89:380-384. [PMID: 18944750 DOI: 10.1094/phyto.1999.89.5.380] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Meloidogyne chitwoodi and M. fallax are serious pests of potato, and both species have been recently designated as quarantine organisms in the European Community and in Canada. The sympatric and less damaging species M. hapla is often found associated with both of them under temperate climates. Here, we describe the use of satellite DNA (satDNA) sequences previously isolated from these three root-knot nematode species for the development of specific diagnostic procedures. In dot-blot experiments, it was unambiguously possible to separate M. chitwoodi and M. fallax from M. hapla using satDNA monomers as probes. In squash-blot experiments, satDNAs allowed discrimination between single individuals of M. chitwoodi or M. fallax from M. hapla, even within root tissues, without the need for DNA purification. The same results were obtained with radioactive or digoxigenin-labeled probes with no loss of sensitivity in detection. M. fallax and M. chitwoodi could not be distinguished. From this study, it is concluded that such cloned satDNA sequences may constitute a powerful tool for the identification and management of Meloidogyne spp. populations in the field and for the implementation of quarantine regulations against these pests.
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Semblat JP, Wajnberg E, Dalmasso A, Abad P, Castagnone-Sereno P. High-resolution DNA fingerprinting of parthenogenetic root-knot nematodes using AFLP analysis. Mol Ecol 1998; 7:119-25. [PMID: 9465419 DOI: 10.1046/j.1365-294x.1998.00326.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amplified fragment length polymorphism (AFLP) analysis has been used to characterize 15 root-knot nematode populations belonging to the three parthenogenetic species Meloidogyne arenaria, M. incognita and M. javanica. Sixteen primer combinations were used to generate AFLP patterns, with a total number of amplified fragments ranging from 872 to 1087, depending on the population tested. Two kinds of polymorphic DNA fragments could be distinguished: bands amplified in a single genotype, and bands polymorphic between genotypes (i.e. amplified in not all but at least two genotypes). Based on presence/absence of amplified bands and pairwise similarity values, all the populations tested were clustered according to their specific status. Significant intraspecific variation was revealed by AFLP, with DNA fragments polymorphic among populations within each of the three species tested. M. arenaria appeared as the most variable species, while M. javanica was the least polymorphic. Within each specific cluster, no general correlation could be found between genomic similarity and geographical origin of the populations. The results reported here showed the ability of the AFLP procedure to generate markers useful for genetic analysis in root-knot nematodes.
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Affiliation(s)
- J P Semblat
- INRA, Laboratoire de Biologie des Invertébrés, Antibes, France
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Grenier E, Castagnone-Sereno P, Abad P. Satellite DNA sequences as taxonomic markers in nematodes of agronomic interest. ACTA ACUST UNITED AC 1997; 13:398-401. [PMID: 15275154 DOI: 10.1016/s0169-4758(97)01113-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The success of alternative crop protection practices against plant-parasitic nematodes using host resistance genes depends fundamentally upon identification of the species and pathotypes effectively controlled by these genes. In the same way, biological control of insects by entomopathogenic nematodes will work only if the nematode strains used are indeed active against the pests to be eliminated. For these applications, the accurate interspecific and/or intraspecific identification of nematodes is thus of outstanding importance. Here, Eric Grenier, Philippe Castagnone-Sereno and Pierre Abad discuss the recent use of satellite DNA sequences in nematode taxonomic diagnostics.
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Affiliation(s)
- E Grenier
- INRA, Laboratoire de Biologie des Inveriébrés, BP 2078, 06606 Antibes Cedex, France
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