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1. Europe as a secondary distribution hub in the worldwide invasion of the potato cyst nematode Globodera rostochiensis

Author: Magali Esquibet, James M. Mwangi, Sebastian Kiewnick, Xiaohong Wang, Benjamin Mimee, Nurul Dwi Handayani, Wim Bert, Johannes Helder, John Wainer, Itaru Sakata, Nathan Garcia, Eric Grenier, and Josselin Montarry
Subjects: Medicine, Science
Abstract: Abstract The potato cyst nematode Globodera rostochiensis originates from the Andean Mountain region in South America and has unintentionally been introduced to all inhabited continents. Several studies have examined the population genetic structure of this pest in various countries by using microsatellite markers. However, merging microsatellite data produced from different laboratories is challenging and can introduce uncertainty when interpreting the results. To overcome this challenge and to explore invasion routes of this pest, we have genotyped 22 G. rostochiensis populations from all continents. Within populations, the highest genetic diversity was observed in the South American populations, the European populations showed an intermediate level of genetic diversity and the remaining populations were the less diverse. This confirmed pre-existing knowledge such as a first introduction event from South America to Europe, but the less diverse populations could originate either from South America or from Europe. At the continental scale, STRUCTURE genetic clustering output indicated that North America and Asia have experienced at least two introduction events. Comparing different evolutionary scenarios, the Approximate Bayesian Computation analysis showed that Europe served as a secondary distribution centre for the invasion of G. rostochiensis into all other continents (North America, Africa, Asia and Oceania).
Published: 2024
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2. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5

Author: Shahid Siddique, Zoran S. Radakovic, Clarissa Hiltl, Clement Pellegrin, Thomas J. Baum, Helen Beasley, Andrew F. Bent, Oliver Chitambo, Divykriti Chopra, Etienne G. J. Danchin, Eric Grenier, Samer S. Habash, M. Shamim Hasan, Johannes Helder, Tarek Hewezi, Julia Holbein, Martijn Holterman, Sławomir Janakowski, Georgios D. Koutsovoulos, Olaf P. Kranse, Jose L. Lozano-Torres, Tom R. Maier, Rick E. Masonbrink, Badou Mendy, Esther Riemer, Mirosław Sobczak, Unnati Sonawala, Mark G. Sterken, Peter Thorpe, Joris J. M. van Steenbrugge, Nageena Zahid, Florian Grundler, and Sebastian Eves-van den Akker
Subjects: Science
Abstract: Plant-parasitic nematodes are a threat to crop production. Combining bioinformatics, genetic and biochemical approaches, the authors show that the plant pathogen beet cyst nematode possesses an incomplete vitamin B5 synthesis pathway, of potential prokaryotic origin, complemented by its plant host.
Published: 2022
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3. Plant–parasite coevolution: A weak signature of local adaptation between Peruvian Globodera pallida populations and wild potatoes

Author: Camille Gautier, Sylvain Fournet, Christophe Piriou, Lionel Renault, Jean‐Claude Yvin, Eric Nguema‐Ona, Eric Grenier, and Josselin Montarry
Subjects: cyst nematode, hatching, local adaptation, Peru, root exudates, wild Solanum species, Ecology, QH540-549.5
Abstract: Abstract Plant–parasite coevolution has generated much interest and studies to understand and manage diseases in agriculture. Such a reciprocal evolutionary process could lead to a pattern of local adaptation between plants and parasites. Based on the phylogeography of each partner, the present study tested the hypothesis of local adaptation between the potato cyst nematode Globodera pallida and wild potatoes in Peru. The measured fitness trait was the hatching of cysts which is induced by host root exudates. Using a cross‐hatching assay between 13 populations of G. pallida and root exudates from 12 wild potatoes, our results did not show a strong pattern of local adaptation of the parasite but the sympatric combinations induced better hatching of cysts than allopatric combinations, and there was a negative relationship between the hatching percentage and the geographical distance between nematode populations and wild potatoes. Moreover, a strong effect of the geographic origin of root exudates was found, with root exudates from south of Peru inducing better hatching than root exudates from north of Peru. These results could be useful to develop new biocontrol products or potato cultivars to limit damages caused by G. pallida.
Published: 2020
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4. The hidden diversity of the potato cyst nematode Globodera pallida in the south of Peru

Author: Romain Thevenoux, Laurent Folcher, Magali Esquibet, Didier Fouville, Josselin Montarry, and Eric Grenier
Subjects: genetic differentiation, genetic diversity, microsatellites, speciation, Evolution, QH359-425
Abstract: Abstract Our knowledge of the diversity of potato cyst nematodes in their native areas still remains patchy and should be improved. A previous study based on 42 Peruvian Globodera pallida populations revealed a clear south to north phylogeographic pattern, with five well‐supported clades and maximum diversity observed in the south of Peru. In order to investigate this phylogeographic pattern more closely, we genotyped a larger collection of Peruvian populations using both cathepsin L gene sequence data and a new set of 13 microsatellite loci. Using different genetic analyses (STRUCTURE, DAPC), we consistently obtained the same results that led to similar conclusions: the presence of a larger genetic diversity than previously known suggesting the presence of cryptic species in the south of Peru. These investigations also allowed us to clarify the geographic borders of the previously described G. pallida genetic clades and to update our knowledge of the genetic structure of this species in its native area, with the presence of additional clades. A distance‐based redundancy analysis (dbRDA) was also carried to understand whether there was a correlation between the population genetic differentiation and environmental conditions. This analysis showed that genetic distances observed between G. pallida populations are explained firstly by geographic distances, but also by climatic and soil conditions. This work could lead to a revision of the taxonomy that may have strong implications for risk assessment and management, especially on a quarantine species.
Published: 2020
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5. Diversity of plant parasitic nematodes characterized from fields of the French national monitoring programme for the Columbia root-knot nematode

Author: Nathan Garcia, Eric Grenier, Alain Buisson, and Laurent Folcher
Subjects: Medicine, Science
Abstract: Plant parasitic nematodes are highly abundant in all agrosystems and some species can have a major impact on crop yields. To avoid the use of chemical agents and to find alternative methods to manage these pests, research studies have mainly focused on plant resistance genes and biocontrol methods involving host plants or natural enemies. A specific alternative method may consist in supporting non-damaging indigenous species that could compete with damaging introduced species to decrease and keep their abundance at low level. For this purpose, knowledge about the biodiversity, structure and functioning of these indigenous communities is needed in order to carry out better risk assessments and to develop possible future management strategies. Here, we investigated 35 root crop fields in eight regions over two consecutive years. The aims were to describe plant parasitic nematode diversity and to assess the potential effects of cultivation practices and environmental variables on communities. Community biodiversity included 10 taxa of plant parasitic nematodes. Despite no significant abundance variations between the two sampling years, structures of communities varied among the different regions. Metadata collected for the past six years, characterizing the cultural practices and soils properties, made it possible to evaluate the impact of these variables both on the whole community and on each taxon separately. Our results suggest that, at a large scale, many variables drive the structuration of the communities. Soil variables, but also rainfall, explain the population density variations among the geographical areas. The effect of the variables differed among the taxa, but fields with few herbicide applications and being pH neutral with low heavy metal and nitrogen concentrations had the highest plant parasitic nematode densities. We discuss how these variables can affect nematode communities either directly or indirectly. These types of studies can help to better understand the variables driving the nematode communities structuration in order to support the abundance of indigenous non-damaging communities that could compete with the invasive species.
Published: 2022

6. Populations of the Beet Cyst Nematode Heterodera schachtii Exhibit Strong Differences in Their Life-History Traits Across Changing Thermal Conditions

Author: Sylvain Fournet, Lucile Pellan, Catherine Porte, Christophe Piriou, Eric Grenier, and Josselin Montarry
Subjects: adaptation, genetic diversity, hatching, specialist/generalist, survival, Microbiology, QR1-502
Abstract: It is widely accepted that climate has an essential influence on the distribution of species and that temperature is the major abiotic factor that affects their life-history traits. Species with very restricted active dispersal abilities and a wide geographical distribution are thus expected to encompass distinct populations adapted to contrasted local conditions. The beet cyst nematode Heterodera schachtii is a good biological model to study temperature adaptation in populations collected from different environments. Here, we tested the effect of temperature on H. schachtii life-history traits using seven field populations from Morocco, Spain, France, Germany, Austria, Poland and Ukraine. We tested hatching and multiplication rates of each population at different temperatures, as well as hatching rates of each population after storage at different temperatures – simulating survival conditions during the inter-cropping period. Results showed a strong temperature effect on the life-history traits explored. Temperature impact on hatching (at different temperatures and after storage at different temperatures) depended on the origin of populations, separating southern from northern ones. Surprisingly, low temperatures influenced hatching less in southern populations. However, for these populations, a storage period at low temperatures strongly reduce subsequent hatching. Conversely, nematode multiplication was not differentially affected by temperatures, as favorable conditions for the host are also favorable for the parasite. Finally, a significant correlation between the genetic diversity and the level of specialization showed that the less diverse populations were more specialized than the more diverse ones.
Published: 2018
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7. The cyst nematode SPRYSEC protein RBP-1 elicits Gpa2- and RanGAP2-dependent plant cell death.

Author: Melanie Ann Sacco, Kamila Koropacka, Eric Grenier, Marianne J Jaubert, Alexandra Blanchard, Aska Goverse, Geert Smant, and Peter Moffett
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: Plant NB-LRR proteins confer robust protection against microbes and metazoan parasites by recognizing pathogen-derived avirulence (Avr) proteins that are delivered to the host cytoplasm. Microbial Avr proteins usually function as virulence factors in compatible interactions; however, little is known about the types of metazoan proteins recognized by NB-LRR proteins and their relationship with virulence. In this report, we demonstrate that the secreted protein RBP-1 from the potato cyst nematode Globodera pallida elicits defense responses, including cell death typical of a hypersensitive response (HR), through the NB-LRR protein Gpa2. Gp-Rbp-1 variants from G. pallida populations both virulent and avirulent to Gpa2 demonstrated a high degree of polymorphism, with positive selection detected at numerous sites. All Gp-RBP-1 protein variants from an avirulent population were recognized by Gpa2, whereas virulent populations possessed Gp-RBP-1 protein variants both recognized and non-recognized by Gpa2. Recognition of Gp-RBP-1 by Gpa2 correlated to a single amino acid polymorphism at position 187 in the Gp-RBP-1 SPRY domain. Gp-RBP-1 expressed from Potato virus X elicited Gpa2-mediated defenses that required Ran GTPase-activating protein 2 (RanGAP2), a protein known to interact with the Gpa2 N terminus. Tethering RanGAP2 and Gp-RBP-1 variants via fusion proteins resulted in an enhancement of Gpa2-mediated responses. However, activation of Gpa2 was still dependent on the recognition specificity conferred by amino acid 187 and the Gpa2 LRR domain. These results suggest a two-tiered process wherein RanGAP2 mediates an initial interaction with pathogen-delivered Gp-RBP-1 proteins but where the Gpa2 LRR determines which of these interactions will be productive.
Published: 2009
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8. The hidden diversity of the potato cyst nematode Globodera pallida in the south of Peru

Author: Magali Esquibet, Laurent Folcher, Romain Thevenoux, Josselin Montarry, Didier Fouville, Eric Grenier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Nématologie (LSV Rennes), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut National de la Recherche Agronomique, Conseil Régional de Bretagne, Anses, European Food Safety Authority (EFSA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Nématologie, and Laboratoire de la Santé des Végétaux
Subjects: 0106 biological sciences, 0301 basic medicine, Species complex, microsatellite, Nematodes, [SDV]Life Sciences [q-bio], Population, lcsh:Evolution, Potato cyst nematode, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, Genetics, lcsh:QH359-425, Globodera pallida, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, Genetic diversity, biology, Original Articles, genetic diversity, 15. Life on land, biology.organism_classification, Phylogeography, 030104 developmental biology, speciation, Evolutionary biology, Genetic structure, Microsatellite, Original Article, genetic differentiation, General Agricultural and Biological Sciences
Abstract: Our knowledge of the diversity of potato cyst nematodes in their native areas still remains patchy and should be improved. A previous study based on 42 Peruvian Globodera pallida populations revealed a clear south to north phylogeographic pattern, with five well‐supported clades and maximum diversity observed in the south of Peru. In order to investigate this phylogeographic pattern more closely, we genotyped a larger collection of Peruvian populations using both cathepsin L gene sequence data and a new set of 13 microsatellite loci. Using different genetic analyses (STRUCTURE, DAPC), we consistently obtained the same results that led to similar conclusions: the presence of a larger genetic diversity than previously known suggesting the presence of cryptic species in the south of Peru. These investigations also allowed us to clarify the geographic borders of the previously described G. pallida genetic clades and to update our knowledge of the genetic structure of this species in its native area, with the presence of additional clades. A distance‐based redundancy analysis (dbRDA) was also carried to understand whether there was a correlation between the population genetic differentiation and environmental conditions. This analysis showed that genetic distances observed between G. pallida populations are explained firstly by geographic distances, but also by climatic and soil conditions. This work could lead to a revision of the taxonomy that may have strong implications for risk assessment and management, especially on a quarantine species.
Published: 2020

9. Image based species identification of Globodera quarantine nematodes using computer vision and deep learning

Author: A. Buisson, Laurent Folcher, Romain Thevenoux, Heloïse Villessèche, Nicolas Parisey, Eric Grenier, Van Linh Le, Marie Beurton-Aimar, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Nématologie (LSV Rennes), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Modélisation Mathématique pour l'Oncologie (MONC), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Institut Bergonié [Bordeaux], UNICANCER-UNICANCER-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), ANSES, Conseil Régional Bretagne, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Institut Bergonié [Bordeaux], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Nématologie, Laboratoire de la Santé des Végétaux, and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)
Subjects: 0106 biological sciences, Species complex, Globodera rostochiensis, Computer science, [SDV]Life Sciences [q-bio], Potato cyst nematode, Horticulture, 01 natural sciences, Convolutional neural network, Automation, Nematode taxonomy, Discriminative model, Machine learning, Globodera pallida, biology, business.industry, Landmarks, Deep learning, Forestry, Pattern recognition, 04 agricultural and veterinary sciences, biology.organism_classification, Computer Science Applications, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Identification (biology), Artificial intelligence, business, Morphometrics, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Identification of plant parasitic nematode species is usually achieved following morphobiometric analysis, which requires a certain level of expertise and remains time consuming. Moreover, molecular and morphological discrimination of a number of emergent or cryptic species is sometimes difficult. Finding a way to achieve morphological characterisation quickly and accurately would greatly advance nematology science. Here, we developed a complete method in order to identify the two quarantine nematode species Globodera pallida and Globodera rostochiensis. First, we chose discriminative metrics on the stylet of nematodes that are able to be used by algorithms in order to build an automated process. Second, we used a custom computer vision algorithm (CCVA) and a convolutional neural network (CNN) to measure our metrics of interest. Third, we compared the CCVA and CNN predictions and their discriminative power to distinguish closely related species. Results show accurate identification of G. pallida and G. rostochiensis with the two methods, despite small-scale divergence (one to five µm depending on the metric used). However, the error rate is higher for Globodera mexicana, suggesting that the algorithms are too specific. Nonetheless, these methods represent a promising novel approach to automated morphological identification of nematodes and Globodera species in particular.
Published: 2021

10. Recent Advances in Population Genomics of Plant-Parasitic Nematodes

Author: Etienne Danchin, Eric Grenier, Josselin Montarry, Georgios Koutsovoulos, Dave T Ste-Croix, Benjamin Mimee, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agriculture and Agri-Food [Ottawa] (AAFC), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Agriculture and Agri-Food (AAFC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest
Subjects: 0106 biological sciences, 0301 basic medicine, Modes of reproduction, Nematoda, [SDV]Life Sciences [q-bio], Population genetics, Genomics, Plant Science, adaptation, Biology, evolutionary genetics, 01 natural sciences, Genome, DNA sequencing, cyst nematodes, Population genomics, 03 medical and health sciences, genomics, Animals, Parasites, root-knot nematodes, genome, Plant Diseases, 2. Zero hunger, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Human evolutionary genetics, food and beverages, population genetics, Plants, plant resistance, 030104 developmental biology, Evolutionary biology, Metagenomics, Adaptation, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Plant-parasitic nematodes are a costly burden of crop production. Ubiquitous in nature, phytoparasitic nematodes are associated with nearly every important agricultural crop and represent a significant constraint on global food security. Population genetics is a key discipline in plant nematology to understand aspects of the life strategies of these parasites, in particular their modes of reproduction, geographic origins, evolutionary histories, and dispersion abilities. Advances in high-throughput sequencing technologies have enabled a recent but active effort in genomic analyses of plant-parasitic nematodes. Such genomic approaches applied to multiple populations are providing new insights into the molecular and evolutionary processes that underpin the establishment of these nematodes and into a better understanding of the genetic and mechanistic basis of their pathogenicity and adaptation to their host plants. In this review, we attempt to update information about genome resources and genotyping techniques useful for nematologists who are thinking about initiating population genomics or genome sequencing projects. This review is intended also to foster the development of population genomics in plant-parasitic nematodes through highlighting recent publications that illustrate the potential for this approach to identify novel molecular markers or genes of interest and improve our knowledge of the genome variability, pathogenicity, and evolutionary potential of plant-parasitic nematodes.
Published: 2021

11. Distribution, DNA barcoding and genetic diversity of potato cyst nematodes in Indonesia

Author: Nurul Dwi Handayani, Marjolein Couvreur, Magali Esquibet, Wim Bert, Johannes Helder, Josselin Montarry, Prabowo Lestari, Eric Grenier, Antarjo Dikin, Universiteit Gent = Ghent University [Belgium] (UGENT), Indonesian Agr Quarantine Agcy, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Indonesian Agency for Agricultural Research and Development Ministry of Agriculture, Wageningen University and Research [Wageningen] (WUR), 1300023185, Ministry of Agriculture, Nature and Food Quality, The Netherlands, Universiteit Gent = Ghent University (UGENT), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Indonesian Agency for Agricultural Research and Development (IAARD)
Subjects: 0106 biological sciences, 0301 basic medicine, Java, Globodera rostochiensis, Zoology, Potato cyst nematode, Plant Science, Horticulture, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, DNA barcoding, Population density, COI, 03 medical and health sciences, parasitic diseases, Globodera, Globodera pallida, Laboratorium voor Nematologie, computer.programming_language, 2. Zero hunger, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Microsatellite, PE&RC, biology.organism_classification, 030104 developmental biology, EPS, Laboratory of Nematology, ITS, Agronomy and Crop Science, computer, 010606 plant biology & botany, Phylogenetic tree
Abstract: International audience; Global trading of plant materials, in combination with agricultural practices, may facilitate the spreading of cyst nematodes to so far non-infected areas. Recently Potato Cyst Nematode (PCN) was recognized to be present in Indonesia and both diversity and distribution require further study. Assessment of PCN populations was done by collecting soil samples, determination of morphological characteristics in combination with ITS rDNA and COI mtDNA sequencing. Thirty-seven soil samples were collected from potato fields in the Indonesia archipelago. The results showed the presence ofGlobodera rostochiensisin 22 out of 37 sampling fields, namely North Sumatra (6 fields), Central Java (12 fields), East Java (3 fields), and -for the first time- in Sulawesi (North Sulawesi) (1 field). The highest observed density was found in Banjarnegara (Central Java), i.e., 872 cysts 100 ml soil(-1).Globodera pallidawas not recovered. Both ITS and COI characterisation of Indonesian PCN (G. rostochiensis) revealed the virtual absence of sequence variation as compared to most PCN from the rest of the world; the COI sequences were identical to the most common and mostly distributed haplotype around the world. Microsatellite genotyping indicated a higher genetic diversity for populations from East Java than for populations from North Sumatra, suggesting that cysts at the origin of populations in North Sumatra were coming from populations in East Java. These data on species identification, population density, genetic diversity, and distribution of potato cyst nematode over the Indonesian archipelago constitute the very basis for the design of environmentally-sound and effective PCN control strategies.
Published: 2020

12. Monitoring and tackling genetic selection in the potato cyst nematode Globodera pallida

Author: Sebastian Kiewnick, Johannes Helder, Josselin Montarry, Aska Goverse, Eric Grenier, Geert Smant, Martijn Holterman, Sylvain Fournet, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Julius Kühn-Institute, Federal Research Centre for Cultivated Plants-Institute for Biological Control, Wageningen University and Research [Wageningen] (WUR), European Project, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Population, Virulence, Potato cyst nematode, Locus (genetics), 01 natural sciences, Life history theory, 03 medical and health sciences, Life Science, Globodera pallida, education, Laboratorium voor Nematologie, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, Food security, biology, business.industry, fungi, Outbreak, food and beverages, biology.organism_classification, Biotechnology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, EPS, Laboratory of Nematology, business, 010606 plant biology & botany
Abstract: International audience; Management of plant pests is probably the most serious challenge in sustainable food production and the maintenance of food security. Due to the strict regulation of or ban on major categories of pesticide, the potato cyst nematode Globodera pallida has been managed by a combination of crop rotation and the potato resistance locus Grp1, a relatively narrow range resistance gene which was introgressed into a range of commercial potato cultivars in Europe. However, in 2014, G. pallida populations were described that can no longer be controlled by Grp1. Most likely similar highly virulent populations will also emerge in all major potato growing areas in North Western Europe where production practices are very similar. Except for laborious, costly and often moderately accurate pot experiments, there is currently no rapid and reliable method to identify virulent populations. This represents a strong limitation and prevents an accurate and durable management of infestations. The PalAdapt project funded by EFSA represents the first step of a European battle plan against the emergence of virulent G. pallida populations and aims at improving the methods and tools for a fast identification of virulence outbreaks. Four main research questions were investigated during the project: (i) Do resistance breaking populations correspond to novel introductions into Europe? (ii) Can miniaturized in vitro tests be used to get more rapidly an accurate identification of the virulence status?, (iii) Is cyst size a life history trait useful to estimate the virulence status of a population?, (iv) Can we identify polymorphism to design molecular tools for an accurate virulence monitoring? The EFSA partnering grants initiative was an accurate way to improve the EU risk assessment capacity through a knowledge exchange among partners having complementary resources and expertise.
Published: 2020

13. Plant–parasite coevolution: A weak signature of local adaptation between Peruvian Globodera pallida populations and wild potatoes

Author: Eric Nguema-Ona, Jean-Claude Yvin, Christophe Piriou, Sylvain Fournet, Lionel Renault, Eric Grenier, Josselin Montarry, Camille Gautier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Mondial d'Innovation - Groupe Roullier (CMI ), Agence de l'Environnement et de la Maitrise de l'Energie, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre Mondial de l'Innovation Roullier, and Groupe Roullier
Subjects: 0106 biological sciences, Biological pest control, Allopatric speciation, Zoology, Potato cyst nematode, 010603 evolutionary biology, 01 natural sciences, root exudates, cyst nematode, 03 medical and health sciences, lcsh:QH540-549.5, hatching, Peru, Globodera pallida, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Nature and Landscape Conservation, Local adaptation, 2. Zero hunger, 0303 health sciences, wild Solanum species, Ecology, biology, Hatching, Host (biology), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, food and beverages, yst nematode, biology.organism_classification, Sympatric speciation, lcsh:Ecology, local adaptation
Abstract: International audience; Plant-parasite coevolution has generated much interest and studies to understand and manage diseases in agriculture. Such a reciprocal evolutionary process could lead to a pattern of local adaptation between plants and parasites. Based on the phylogeography of each partner, the present study tested the hypothesis of local adaptation between the potato cyst nematode Globodera pallida and wild potatoes in Peru. The measured fitness trait was the hatching of cysts which is induced by host root exudates. Using a cross-hatching assay between 13 populations of G. pallida and root exudates from 12 wild potatoes, our results did not show a strong pattern of local adaptation of the parasite but the sympatric combinations induced better hatching of cysts than allopatric combinations, and there was a negative relationship between the hatching percentage and the geographical distance between nematode populations and wild potatoes. Moreover, a strong effect of the geographic origin of root exudates was found, with root exudates from south of Peru inducing better hatching than root exudates from north of Peru. These results could be useful to develop new biocontrol products or potato cultivars to limit damages caused by G. pallida.
Published: 2020

14. Evidence of strong gene flow among French populations of the carrot cyst nematode Heterodera carotae

Author: Christophe Piriou, Magali Esquibet, Eric Grenier, Camille Gautier, Josselin Montarry, Sylvain Fournet, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, normandie, AMOVA, education, isolation by distance, flux de gènes, Plant Science, Horticulture, Biology, migration, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, Botany, Genetics, medicine, genetic structure, Cyst, health care economics and organizations, 030304 developmental biology, 0303 health sciences, fungi, heterozygote deficit, food and beverages, hetérodéra carotae, microsatellite markers, medicine.disease, biology.organism_classification, structure génétique, Nematode, marqueur microsatellite, nématode phytoparasite, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science, microsatellite repeats, france, Heterodera carotae
Abstract: International audience; Evidence of strong gene flow among French populations of the carrot cyst nematode [i]Heterodera carotae[/i]
Published: 2020

15. Exploring the causes of small effective population sizes in cyst nematodes using artificial Globodera pallida populations

Author: Josselin Montarry, Sylvain Fournet, Pierre-Loup Jan, Eric J. Petit, Eric Grenier, Romain Mabon, Sylvie Bardou-Valette, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, Evolution, nematode, [SDV]Life Sciences [q-bio], Population, Zoology, selection, Potato cyst nematode, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Effective population size, Genetic drift, medicine, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cyst, [INFO]Computer Science [cs], Tylenchoidea, Globodera pallida, education, Selection (genetic algorithm), Plant Diseases, Solanum tuberosum, 030304 developmental biology, General Environmental Science, Population Density, 0303 health sciences, education.field_of_study, General Immunology and Microbiology, biology, General Medicine, biology.organism_classification, medicine.disease, plant resistance, Nematode, [SDE]Environmental Sciences, genetic drift, General Agricultural and Biological Sciences, effective population size
Abstract: The effective size of a population is the size of an ideal population which would undergo genetic drift at the same rate as the real population. The balance between selection and genetic drift depends on the effective population size (Ne), rather than the real numbers of individuals in the population (N). The objectives of the present study were to estimateNein the potato cyst nematodeGlobodera pallidaand to explore the causes of a lowNe/Nratio in cyst nematodes using artificial populations. Using a temporal analysis of 24 independent populations, the medianNewas 58 individuals (minNe= 25 and maxNe= 228).Neis commonly lower thanNbut in the case of cyst nematodes, theNe/Nratio was extremely low. Using artificial populations showed that this low ratio did not result from migration, selection and overlapping generations, but could be explain by the fact thatG. pallidapopulations deviate in structure from the assumptions of the ideal population by having unequal sex ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a lowNe, resulting in a strong intensity of genetic drift, could be important for their control becauseG. pallidapopulations will have a low capacity to adapt to changing environments.
Published: 2019

16. What determines host specificity in hyperspecialized plant parasitic nematodes?

Author: Etienne Lord, Michael Sabeh, Benjamin Mimee, Eric Grenier, Marc St-Arnaud, Agriculture and Agri-Food Canada (AAFC), Université de Montréal (UdeM), Jardin Botanique de Montréal, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), 2015-69004-23634, National Institute of Food and Agriculture, n.a., Agriculture and Agri-Food Canada, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Agriculture and Agri-Food [Ottawa] (AAFC), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Agriculture and Agri-Food (AAFC), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, effecteur, RNA-Seq, Polymerase Chain Reaction, 01 natural sciences, Transcriptome, Transcriptomic study, ComputingMilieux_MISCELLANEOUS, Regulator gene, nématode à kyste, 2. Zero hunger, Genetics, 0303 health sciences, gamme d'hôtes, Effector, globodera, effector, Plant-parasitic nematode, Research Article, Biotechnology, lcsh:QH426-470, Globodera rostochiensis, lcsh:Biotechnology, hosts range, Virulence, Biology, Host Specificity, 03 medical and health sciences, lcsh:TP248.13-248.65, Invertebrate Zoology, Effectors, Globodera, Host range, Pathogenicity, RNA-seq, Animals, Tylenchoidea, Gene, Solanum tuberosum, 030304 developmental biology, Sequence Analysis, RNA, Host (biology), Gene Expression Profiling, Genetic Variation, biology.organism_classification, Zoologie des invertébrés, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, lcsh:Genetics, 010606 plant biology & botany
Abstract: Background In hyperspecialized parasites, the ability to grow on a particular host relies on specific virulence factors called effectors. These excreted proteins are involved in the molecular mechanisms of parasitism and distinguish virulent pathogens from non-virulent related species. The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida are major plant-parasitic nematodes developing on numerous solanaceous species including potato. Their close relatives, G. tabacum and G. mexicana are stimulated by potato root diffusate but unable to establish a feeding site on this plant host. Results RNA sequencing was used to characterize transcriptomic differences among these four Globodera species and to identify genes associated with host specificity. We identified seven transcripts that were unique to PCN species, including a protein involved in ubiquitination. We also found 545 genes that were differentially expressed between PCN and non-PCN species, including 78 genes coding for effector proteins, which represent more than a 6-fold enrichment compared to the whole transcriptome. Gene polymorphism analysis identified 359 homozygous non-synonymous variants showing a strong evidence for selection in PCN species. Conclusions Overall, we demonstrated that the determinant of host specificity resides in the regulation of essential effector gene expression that could be under the control of a single or of very few regulatory genes. Such genes are therefore promising targets for the development of novel and more sustainable resistances against potato cyst nematodes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5853-4) contains supplementary material, which is available to authorized users.
Published: 2019

17. Phenotypic and Genomic Modifications Associated with Globodera pallida Adaptation to Potato Resistances

Author: Delphine Eoche-Bosy, Sylvain Fournet, Eric Grenier, Marie-Claire Kerlan, Josselin Montarry, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 0301 basic medicine, résistance aux maladies, globodera pallida, Virulence, Genome Scan, Potato cyst nematode, Locus (genetics), Quantitative trait locus, 01 natural sciences, 03 medical and health sciences, analyse de génome, résistance aux agents pathogènes, pomme de terre, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Globodera pallida, adaptation des plantes, Local adaptation, Nematode, nématode à kyste, 2. Zero hunger, Genetics, Experimental evolution, biology, résistance quantitative, food and beverages, biology.organism_classification, virulence, resistance to diseases, 030104 developmental biology, potato, Genome scan, Resistance durability, Agronomy and Crop Science, 010606 plant biology & botany, Food Science
Abstract: Studying phenotypic and genomic modifications associated with pathogen adaptation to resistance is a crucial step to better understand and anticipate resistance breakdown. This short review summarizes recent results obtained using experimentally evolved populations of the potato cyst nematode Globodera pallida. In a first step, the variability of resistance durability was explored in four different potato genotypes carrying the resistance quantitative trait loci (QTL) GpaV(vrn) originating from Solanum vernei but differing by their genetic background. The consequences of the adaptation to resistance in terms of local adaptation, cross-virulence and virulence cost were then investigated. Finally, a genome scan approach was performed in order to identify the genomic regions involved in this adaptation. Results showed that nematode populations were able to adapt to the QTL GpaV(vrn), and that the plant genetic background has a strong impact on resistance durability. A trade-off between the adaptations to different resistant potato genotypes was detected, and we also showed that adaptation to the resistance QTL GpaV(vrn) from S. vernei did not allow adaptation to the colinear locus from S. sparsipilum (GpaV(spl)). Unexpectedly, the adaptation to resistance led to an increase of virulent individual's fitness on a susceptible host. Moreover, the genome scan approach allowed the highlighting of candidate genomic regions involved in adaptation to host plant resistance. This review shows that experimental evolution is an interesting tool to anticipate the adaptation of pathogen populations and could be very useful for identifying durable strategies for resistance deployment.
Published: 2018

18. Impact of native plant-parasitic nematode communities on the establishment of Meloidogyne chitwoodi

Author: N. Garcia, Fabrice Ollivier, Laurent Folcher, A. Buisson, C. Sarniguet, Eric Grenier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Brittany Regional Council, French Agency for Food, Environmental and Occupational Health & Safety, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, competition phenomenon, Plant Science, Horticulture, 01 natural sciences, nématode parasite, quarantine species, 03 medical and health sciences, pomme de terre, Botany, Genetics, biology, meloidogyne chitwoodi, parasite de quarantaine, Native plant, biology.organism_classification, plant-parasitic nematode communities, 030104 developmental biology, Nematode, Meloidogyne chitwoodi, potato, Agronomy and Crop Science, original experimental design, compétition interspécifique, 010606 plant biology & botany
Abstract: Among plant-parasitic nematodes (PPNs), the species Meloidogyne chitwoodi constitutes an important agricultural issue and is listed as a quarantine species in the EU. This study investigated whether PPN communities can affect the establishment and expansion of M. chitwoodi during a simulated introduction. An original experimental design was developed on potato in the glasshouse involving four PPN communities derived from a single natural one that was initially grown on different host plants. Meloidogyne chitwoodi was inoculated at two different densities (50 or 1000 second-stage juveniles (J2) per pot). After 4 months, M. chitwoodi was more abundant in the community showing a low overall abundance of PPNs, decreased in the other PPN communities and failed to establish in five pots out of 80. Results showed that establishment - even starting from a very low inoculum - can occur in all communities even if indigenous PPNs in the community affect the expansion through interspecific competition. The reverse interaction was also observed as PPN taxa were generally less abundant in the 1000 M. chitwoodi J2 inoculation treatments. The proportion of M. chitwoodi males produced was higher in the community showing low overall PPN abundance, suggesting a strong sensitivity of M. chitwoodi to intraspecific competition. The presented results suggest that a low abundance of indigenous PPNs presents a higher risk of expansion of M. chitwoodi even if the introduced inoculum is low.
Published: 2018

19. Impact of agricultural practices and environmental variables on plant-parasitic nematode communities in fields at a landscape scale

Author: Benoit Ricci, Nathan Garcia, Agathe Maupetit, Luc Biju-Duval, Eric Grenier, Laurent Folcher, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université Bretagne Loire (UBL), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Interactions Arbres-Microorganismes (IAM), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: 0106 biological sciences, oilseed rape, media_common.quotation_subject, multiple correspondence analysis, Biology, 01 natural sciences, Multiple correspondence analysis, Abundance (ecology), [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecology, Evolution, Behavior and Systematics, media_common, agriculture, 2. Zero hunger, nematode abundance, Community, business.industry, Ecology, model averaging, 04 agricultural and veterinary sciences, 15. Life on land, Crop rotation, Tillage, Taxon, Agriculture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Psychological resilience, France, business, Agronomy and Crop Science, community ecology, 010606 plant biology & botany
Abstract: International audience; Agricultural practices shaping plant-parasitic nematode (PPN) assembly are still unclear, and this limits our understanding of the impact of anthropic disturbances on the resilience of PPN communities and the emergence of agronomic problems. Here the abundance and diversity of PPN in France's oilseed rape production area was determined by sampling 72 fields over two consecutive years. We identified and counted PPN taxa and collected anthropic and environmental variables for the past 5 years. PPN were assigned to seven genera and one family including PPN that have not been identified to genus level. Using multiple correspondence analyses, we selected the main variables and tested their effect on the abundance of each taxon with mixed generalised linear models. We emphasise that at the landscape scale investigated, crop rotations were no longer a major factor impacting the PPN communities. However, we observed that tillage and pesticides had a significant impact on several taxa.
Published: 2018

20. Effective population size and durability of plant resistances in the potato cyst nematode Globodera pallida

Author: Eric J. Petit, Pierre-Loup Jan, Josselin Montarry, Eric Grenier, Sylvain Fournet, Sylvie Bardou-Valette, and Romain Mabon
Subjects: education.field_of_study, biology, Genetic drift, Agronomy, Effective population size, Population size, Population, Potato cyst nematode, Globodera pallida, biology.organism_classification, education, Inbreeding, Selection (genetic algorithm)
Abstract: SummaryThe effective size of a population is the size of an ideal population which would drift at the same rate as the real population. The balance between selection and genetic drift depends on the population size expressed as the genetically effective population size (Ne), rather than the real numbers of individuals in the population (N).The objectives of the present study were to estimate Nein the potato cyst nematodeGlobodera pallidausing artificial populations and to explore the link between Neand the durability of plant resistances.Using a temporal method on 24 independent pairs of initial and final populations, the median Newas 58 individuals.Neis commonly lower than N but in our case the Ne/N ratio was extremely low becauseG. pallidapopulations deviate in structure from the assumptions of the ideal population by having unequal sex-ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a low Necould be important for the control of phytoparasitic nematodes becauseG. pallidapopulations will have a low capacity to adapt to changing environments unless selection intensity is very strong, which could be greatly beneficial for long-term use of plant resistances.
Published: 2017
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21. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida

Author: Delphine Eoche-Bosy, Magali Esquibet, Eric Grenier, Matthieu Gautier, Josselin Montarry, Olivier Bouchez, Anthony Bretaudeau, Fabrice Legeai, Sylvain Fournet, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Plateforme bioinformatique GenOuest [Rennes], Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)
Subjects: 0301 basic medicine, population genomics, Genome Scan, selection, evolve and resequence, Potato cyst nematode, Genomics, Polymorphism, Single Nucleotide, Genome, Population genomics, 03 medical and health sciences, Genetics, Animals, Tylenchoidea, experimental evolution, Globodera pallida, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Disease Resistance, Solanum tuberosum, 2. Zero hunger, Experimental evolution, Models, Genetic, biology, Pool-Seq, food and beverages, biology.organism_classification, virulence, Genetics, Population, 030104 developmental biology, Genetic marker, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaV(vm), has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a) virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.
Published: 2017

22. Experimentally evolved populations of the potato cyst nematode Globodera pallida allow the targeting of genomic footprints of selection due to host adaptation

Author: Josselin Montarry, Jérémy Gauthier, Delphine Eoche-Bosy, Sylvain Fournet, Eric Grenier, Magali Esquibet, Amandine Suzanne Juhel, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique, and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0301 basic medicine, Genetics, Experimental evolution, biology, Genome Scan, food and beverages, Potato cyst nematode, Context (language use), Plant Science, genome scan, Horticulture, biology.organism_classification, Genome, outlier, resistance, virulence, 03 medical and health sciences, 030104 developmental biology, Polymorphic Microsatellite Marker, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Host adaptation, experimental evolution, Globodera pallida, Agronomy and Crop Science
Abstract: In the current agronomical context of pesticide use reduction, deciphering the genetic bases of pathogen adaptation to plant resistances is of major importance to improve their durability. Knowledge of the virulence gene frequencies in pathogens populations could indeed allow the prediction of their durability before deployment. Globodera pallida is a major pest of potato crop for which a promising resistance QTL, GpaVvrn, has been identified in Solanum vernei. An experimental evolution study, in which G. pallida lineages evolved on resistant or susceptible potato genotypes for up to eight generations, previously showed that G. pallida was able to rapidly overcome GpaVvrn resistance. However it was not known if enough genetic mixing occurred in these lineages to be able to detect islands of differentiation in a genome scan approach. Here, we investigated this question using 53 polymorphic microsatellite markers distributed along the genome and three different tests based on genetic differentiation and heterozygosity. We identified eight outlier loci, indicative of genomic regions putatively involved in host adaptation. Several loci were identified by multiple detection methods and/or in two independent adapted lineages. We also showed that some identified candidate genomic regions seem to be also involved in the overcoming of nematode resistance in a genotype harbouring the same resistance QTL in a different genetic background. These results validate the feasibility of a genome scan approach on a biological material coming from short experimental evolution, and encourage to perform a high coverage genome scan using whole genome resequencing. This article is protected by copyright. All rights reserved.
Published: 2017

23. Genome scans on experimentaly evolved globodera pallida populations to identify molceular basis of adaptation to GPAV(VRN) potato resistance

Author: Delphine Eoche-Bosy, Magali Esquibet, Sylvain Fournet, Mathieu Gautier, Fabrice Legeai, Anthony Bretaudeau, Eric Grenier, Josselin Montarry, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: [SDV]Life Sciences [q-bio], fungi, food and beverages
Abstract: In the current agronomical context of reduced use of pesticides, deciphering the genetic bases of pathogen adaptation to plant resistances is of major importance as it could help us to improve durability of these resistances. Globodera pallida is a major pest of potato and for which the promising resistance factor, QTL GpaVvrn, has been identified in Solanum vernei and introduced into several new resistant cultivars in Europe.
Published: 2016

24. Genetic structure and evolution of potato cyst nematodes populations

Author: Eric Grenier, Y Veronneau, P., Lafond-Lapalme, J., Josselin Montarry, Sylvain Fournet, Mimee, B., Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Agriculture and Agri-Food (AAFC), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Agriculture and Agri-Food [Ottawa] (AAFC), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: [SDV]Life Sciences [q-bio], fungi, food and beverages
Abstract: To understand the mechanisms leading to the breakdown of plant resistance by potato cyst nematodes (PCN; Globodera rostochiensis and G. pallida), an understanding of the genetic structure and variation in populations and the processes that govern their evolution is required.
Published: 2016

25. Occurrence of the tobacco cyst nematode subspecies Globodera tabacum subsp virginiae in France

Author: Josselin Montarry, Sylvie Bardou-Valette, Eric Grenier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), INRA SPE, AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, 0301 basic medicine, Nicotiana tabacum, [SDV]Life Sciences [q-bio], Principal component analysis, Plant Science, Horticulture, Subspecies, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Cleaved amplified polymorphic sequence, Botany, Globodera tabacum, biology, fungi, food and beverages, Microsatellite, biology.organism_classification, 030104 developmental biology, Nematode, Genetic marker, Ploidy, Agronomy and Crop Science, Plant-parasitic nematode
Abstract: International audience; Tobacco cyst nematode is a sexually diploid species composed of three subspecies, Globodera tabacum subsp. tabacum (Gtt), G. tabacum subsp. virginiae (Gtv) and G. tabacum subsp. solanacearum (Gts). In Europe, only Gtt have been reported to date. Here, we report from a plant in a French tobacco field, the identification of a mixture between cysts of the subspecies Gtt and cysts genetically different. The objective of the present study was to determine the subspecies status of those particular cysts. To this aim, we performed CAPS analyses on two genes and a principal component analysis on microsatellite data. The results obtained with both CAPS and microsatellite markers demonstrate for the first time the occurrence of G. tabacum subsp. virginiae in France.
Published: 2016

26. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Author: Pasqua Veronico, Emeline Deleury, Francesca De Luca, Magali Esquibet, Patrick Wincker, Thomas J. Baum, Tom R. Maier, Erika Sallet, Jonathan J. Ewbank, Edgardo Ugarte, Cyril Van Ghelder, Marie-Noëlle Rosso, Delphine Steinbach, Marie-Cécile Caillaud, Jean Weissenbach, Véronique Anthouard, Pedro M. Coutinho, Mark Blaxter, Jean-Marc Aury, Marc Robinson-Rechavi, Pierre Abad, Geert Smant, Timothé Flutre, Hadi Quesneville, Gabriel V. Markov, Paul McVeigh, Jérôme Gouzy, Philippe Castagnone-Sereno, Corinne Dasilva, Etienne Danchin, Paola Leonetti, Aaron G. Maule, Marc Magliano, Béatrice Ségurens, John T. Jones, Eric L. Davis, Laetitia Perfus-Barbeoch, Claire Jubin, Thomas Schiex, Vincent Laudet, Florence Deau, Olivier Jaillon, François Artiguenave, Eric Grenier, Tarek Hewezi, Bruno Favery, Teresa Bleve-Zacheo, T.O.G. Tytgat, Bernard Henrissat, Noureddine Hamamouch, Graziano Pesole, Jared V. Goldstone, Julie Poulain, Vivian C. Blok, Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Scottish Crop Research Institute, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Istituto per la Protezione delle Piante, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Unité de Recherche Génomique Info (URGI), Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), Department of Plant Pathology, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Iowa State University (ISU), School of Biological Sciences, Dipartimento di Biochimica e Biologia moleculare, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Department of Ecology and Evolution, Université de Lausanne = University of Lausanne (UNIL), Laboratory of Nematology, Wageningen University and Research [Wageningen] (WUR), Institute of Evolutionary Biology, University of Edinburgh, University of North Carolina System (UNC), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, School of Biolgical Sciences, Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR 1064 UMR INRA / CNRS / Univ. Nice (Univ.SA) : Interactions Plantes Microorganismes et Santé Végétale, Institut National de la Recherche Agronomique (INRA)-Santé des plantes et environnement (S.P.E.)-UMR INRA / CNRS / Univ. Nice (Univ.SA) : Interactions Plantes Microorganismes et Santé Végétale, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Consiglio Nazionale delle Ricerche [Roma] (CNR), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Università degli studi di Bari, Université de Lausanne (UNIL), Wageningen University and Research Centre [Wageningen] (WUR), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Unité de Biométrie et Intelligence Artificielle (UBIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Università degli studi di Bari Aldo Moro (UNIBA)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Helminth genetics, 01 natural sciences, Applied Microbiology and Biotechnology, Genome, Plant Roots, Meloidogyne incognita, ADAPTATION, genes, root-knot nematodes, Genes, Helminth, 2. Zero hunger, Expressed Sequence Tags, 0303 health sciences, biology, plant-parasitic nematode, EPS-2, Chromosome Mapping, GENOME SEQUENCE, food and beverages, DNA, Helminth, Plants, bdelloid rotifers, MELOIDOGYNE INCOGNITA, PARTHENOGENETIC NEMATODE, Molecular Medicine, RNA Interference, Terra incognita, Biotechnology, DNA, Complementary, Sequence analysis, Molecular Sequence Data, Biomedical Engineering, cloning, Bioengineering, phytopathogenic bacteria, 03 medical and health sciences, Botany, expression, Animals, Tylenchoidea, Gene, Laboratorium voor Nematologie, 030304 developmental biology, Plant Diseases, Whole genome sequencing, PLANT PARASITISM, Genome, Helminth, Base Sequence, Sequence Analysis, DNA, prediction, biology.organism_classification, caenorhabditis-elegans, Nematode, Evolutionary biology, identification, Laboratory of Nematology, protein, Sequence Alignment, 010606 plant biology & botany
Abstract: Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies
Published: 2008

27. Heterozygote deficits in cyst plant-parasitic nematodes: possible causes and consequences

Author: Sylvain Fournet, Andrew Overall, Eric J. Petit, Sylvie Bardou-Valette, Eric Olivier, Cécile Gracianne, Josselin Montarry, Pierre-Loup Jan, Eric Grenier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, School of Pharmacy and Biomedical Sciences, University of Brighton, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, Heterozygote, microsatellite, Genotype, Wahlund effect, nematode, Consanguinity, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, consanguinity, Gene Frequency, Tobacco, Genetics, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Inbreeding, Tylenchoidea, Globodera pallida, Ecology, Evolution, Behavior and Systematics, Alleles, 030304 developmental biology, Solanum tuberosum, 0303 health sciences, Likelihood Functions, fungi, heterozygote deficit, Genetic Variation, food and beverages, Heterozygote advantage, biology.organism_classification, Null allele, Genetics, Population, null allele, Biological dispersal, Beta vulgaris, Heterodera schachtii, Microsatellite Repeats
Abstract: International audience; Deviations of genotypic frequencies from Hardy-Weinberg equilibrium (HWE) expectations could reveal important aspects of the biology of populations. Deviations from HWE due to heterozygote deficits have been recorded for three plant-parasitic nematode species. However, it has never been determined whether the observed deficits were due (i) to the presence of null alleles, (ii) to a high level of consanguinity and/or (iii) to a Wahlund effect. The aim of the present work was, while taking into the possible confounding effect of null alleles, to disentangle consanguinity and Wahlund effect in natural populations of those three economically important cyst nematodes using microsatellite markers: Globodera pallida, G. tabacum and Heterodera schachtii, pests of potato, tobacco and sugar beet, respectively. The results show a consistent pattern of heterozygote deficiency in the three nematode species sampled at the spatial scale of the host plant. We demonstrate that the prevalence of null alleles is weak and that heterozygote deficits do not have a single origin. Our results suggested that it is restricted dispersal that leads to heterozygote deficits through both consanguinity and substructure, which effects can be linked to soil movement, cyst density, and the number of generations per year. We discuss potential implications for the durability of plant resistances that are used to protect crops against parasites in which mating between relatives occur. While consanguineous mating leads to homozygosity at all loci, including loci governing avirulence/virulence, which favours the expression of virulence when recessive, the Wahlund effect is expected to have no particular effect on the adaptation of nematodes to resistances.
Published: 2015

28. Heterozygote deficits in cyst forming plant parasitic nematodes: disentangling consanguinity and Wahlund effect

Author: Josselin Montarry, Pierre-Loup Jan, Cécile Gracianne, Sylvie Bardou-Valette, Sylvain Fournet, Eric Grenier, Eric Petit, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: microsatellite, consanguinity, Wahlund effect, nematode, [SDV]Life Sciences [q-bio], heterozygote deficit
Abstract: Session 6: GenomicsSession 6: Genomics; absent
Published: 2014

29. Human influence on the dispersal and genetic structure of French Globodera tabacum populations

Author: Josselin Montarry, Eric Grenier, Charline Alenda, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), INRA (Institut National de la Recherche Agronomique), ANITTA (Association Nationale Interprofessionnelle et Technique du Tabac), Imperial Tobacco - ALTADIS, ARN (Association pour la Recherche sur les Nicotianees) [3582], Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: Microbiology (medical), Population genetics, [SDV]Life Sciences [q-bio], Population, Population Dynamics, Tobacco cyst nematode, Microbiology, Linkage Disequilibrium, Genetic diversity, Gene flow, Genetics, Animals, Cluster Analysis, Humans, Human Activities, Genetic variability, Tylenchoidea, Globodera tabacum, education, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, education.field_of_study, biology, Geography, Ecology, fungi, Genetic Variation, Microsatellite, Agriculture, Bayes Theorem, 15. Life on land, biology.organism_classification, Infectious Diseases, Genetics, Population, Genetic structure, Biological dispersal, France, Microsatellite Repeats
Abstract: International audience; The dispersal abilities and the population genetic structure of nematodes living in soils are poorly known. In the present study, we have pursued these issues in the tobacco cyst nematode, Globodera tabacum, which is responsible of significant yield reductions. Nine microsatellites markers were used to explore the dispersal and genetic structure of 18 French G. tabacum populations. All the populations sampled belong to the "tabacum" subspecies and low level of gene flow was observed among G. tabacum populations in France. Bayesian genetic assignments revealed two distinct genetic groups that matched with the geographic limits of two agricultural cooperative societies. An important part of the genetic variability was observed between these agricultural cooperative societies and also within populations. Those results highlight the impact of the human organization of agricultural practices on the genetic structure of G. tabacum populations and complement previous results obtained on other cyst nematodes, showing the major contribution of human activities and soil transports during harvest in the passive dispersion of these organisms. (c) 2014 Elsevier B.V. All rights reserved.
Published: 2014

30. Genetic diversity of the golden potato cyst nematode Globodera rostochiensis and determination of the origin of populations in Quebec, Canada

Author: Josselin Montarry, Benjamin Mimee, Peter Moffett, Eric Grenier, Annie Christine Boucher, Guy Bélair, Sylvie Bardou-Valette, Agriculture and Agri-Food (AAFC), Département de biologie [Sherbrooke] (UdeS), Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Centre de Recherche Les Buissons Inc. through Agriculture and Agri-food Canada Growing Canadian Agri-Innovations Program, Institut National de la Recherche Agronomique, Fonds de Recherche Quebecois Nature et Technologie, Centre SEVE, National Sciences and Engineering Research Council, Agriculture and Agri-Food [Ottawa] (AAFC), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Dept Biol, and Sherbrooke University
Subjects: 0106 biological sciences, Population genetics, [SDV]Life Sciences [q-bio], MULTILOCUS GENOTYPE DATA, LOCI, Potato cyst nematode, 01 natural sciences, PALLIDA, NUMBER, PROGRAM, Phylogeny, 0303 health sciences, education.field_of_study, biology, Ecology, Quebec, Phylogeography, Phenotype, DIFFERENTIATION, Genetic structure, Bolivia, Multiple introductions, Genotype, Globodera rostochiensis, Population, education, New York, 03 medical and health sciences, Genetics, Animals, Tylenchoidea, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Plant Diseases, Solanum tuberosum, 030304 developmental biology, Life Cycle Stages, Genetic diversity, MICROSATELLITE MARKERS, Genetic Variation, Microsatellite, Sequence Analysis, DNA, biology.organism_classification, INDIVIDUALS, Genetics, Population, Nematode, EUROPEAN POPULATIONS, INFERENCE, PEST analysis, Introduced Species, Microsatellite Repeats, 010606 plant biology & botany
Abstract: International audience; The golden cyst nematode (Globodera rostochiensis), native to South America, has been introduced in many parts of the world, including Europe and North America. Recently, it was found for the first time in the province of Quebec, Canada in the locality of St. Amable near Montreal. To date, very few studies have examined the population genetics of this pest. Consequently, there is a lack of knowledge about the genetic structure and evolution of this nematode. In this study, twelve new microsatellite markers were developed in order to explore these questions. These markers were used to genotype fifteen populations originating from different regions of the world, including five from Canada. Within populations, the highest genetic diversity was consistently observed in the populations from Bolivia, the postulated region of origin of the golden nematode, and the lowest in populations from British Columbia (Canada) and New York (USA). The two Quebec populations were very similar to each other and to the population found in Newfoundland, but surprisingly, they were significantly different from three other North American populations including those from New York and British Columbia. Based on our results, we conclude that the golden cyst nematode has been introduced in North America at least twice from distinct regions of the world. Crown Copyright (C) 2013 Published by Elsevier Inc. All rights reserved.
Published: 2013

31. Variability among tobacco cyst nematode subspecies and consequences on their sustainable management with host resistances

Author: Alenda, Charline, Fouville, D., Gallot, A., Mariette, N., Eric Grenier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Association Nationale Interprofessionnelle et Technique du Tabac (ANITTA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: tobacco cyst nematode, [SDV]Life Sciences [q-bio]
Abstract: absent
Published: 2012

32. Genetic structure of golden nematode populations from Québec, Canada, with the use of new microsatellite markers

Author: Boucher, Annie Christine, Mimee, B., Montarry, J., Belair, G., Moffett, P., Eric Grenier, Agriculture and Agri-Food [Ottawa] (AAFC), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Sherbrooke University, Agriculture and Agri-Food (AAFC), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Sherbrooke (UdeS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ProdInra, Archive Ouverte
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: absent
Published: 2012

33. An evaluation of the implications of virulence in non-European populations of Globodera pallida and G. rostochiensis for potato cultivation in Europe

Author: Bjoern Niere, Jon Pickup, Géraldine Anthoine, Nicole Viaene, Loes den Nijs, Sue Hockland, Eric Grenier, Vivian C. Blok, Mark S. Phillips, Food & Environm Res Agcy, Inst Natl & Int Plant Hlth, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), The James Hutton Institute, Plant Protection Service, Plant Hlth Lab, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Science and Advice for Scottish Agriculture, Research Institute for Agricultural, Fisheries and Food (ILVO), Food and Environment Research Agency, Belgian Plant Protection Service (FAVV) [10-ILVOCRA-Planten], Scottish Government RE-SAS (Rural and Environment Science and Analytical Services), Julius Kühn Institute (JKI), Institute for Agricultural and Fisheries Research, and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Population, SOLANUM-VERNEI, Biology, 01 natural sciences, CYST-NEMATODES, law.invention, 03 medical and health sciences, PATHOTYPES, law, Quarantine, Cultivar, Genetic variability, ANDES, Globodera pallida, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Nematology, education.field_of_study, Resistance (ecology), fungi, quarantine, food and beverages, biology.organism_classification, GENE, VARIABILITY, Nematode, Agronomy, phytosanitary measures, potato cyst nematodes, Agronomy and Crop Science, RESISTANCE, 010606 plant biology & botany
Abstract: Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; The potato cyst nematodes Globodera pallida and G. rostochiensis are listed in the EU Plant Health Directive 2000/29/EC and are also subject to the new EU Council Directive 2007/33/EC on the control of potato cyst nematodes, requiring unilateral suppression of these pests in Europe. At the same time there is also pressure to increase world trade in potatoes. Such pressure has to be balanced by the risks involved in the associated spread of these pests and subsequent problems in management. Populations of the potato cyst nematodes from outside Europe, in particular South America, which is considered the origin of G. pallida and G. rostochiensis, pose a risk to those European countries where limited genetic variability of these nematode species has been recorded. The development and usage of resistant cultivars under such conditions has formed a pivotal role in integrated management programmes in Europe. Molecular studies have shown that populations of G. pallida and G. rostochiensis from South America have a different genetic composition from those in Europe. The introduction of such populations would pose a threat to the use of resistant cultivars as a major tool in reducing the potential spread and damage caused by these species. At present, an inability to link precisely genetic variability to the virulence characteristics of a specific nematode population, and quickly identify the virulence status of intercepted populations for inspection purposes, strengthens the case for using plant health legislation to prevent their introduction.
Published: 2012

34. Other Nematode Effectors and Evolutionary Constraints

Author: Eric Grenier, Marie-Noëlle Rosso, Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Jones, J., Gheysen, G., Fenoll, C., and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0303 health sciences, biology, Host (biology), Effector, fungi, Virulence, Plant Immunity, Parasitism, food and beverages, biology.organism_classification, Plant cell, 01 natural sciences, 03 medical and health sciences, Nematode, Evolutionary biology, Secretion, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Like microbial pathogens, nematodes secrete a repertoire of effectors with diverse functions. In the case of sedentary nematodes, completion of the life cycle requires the maintenance of the biotrophic interaction for several weeks and the induction of a permanent feeding site. These essential processes require fine tuning of plant cell responses. About a hundred candidate effectors have been isolated from nematodes to date that have roles in the invasion of host tissues, evasion of plant defences, suppression of plant defences or manipulation of plant cell fate. Evolutionary studies suggest that several distinct mechanisms have led to the acquisition of these effectors during the evolution of plant parasitism. In addition, since any compound secreted by the parasite can potentially be perceived as nonself by the plant, nematode effectors are subject to selective pressure to escape plant immunity. This chapter reviews the latest findings on nematode effector functions and evolutionary traits.
Published: 2011
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35. Molecular Variability and Evolution of the Pectate Lyase (pel-2) Parasitism Gene in Cyst Nematodes Parasitizing Different Solanaceous Plants

Author: Barbara Gerič Stare, G. Urek, Saša Širca, Didier Fouville, Aurore Gallot, Eric Grenier, Agricultural Institute of Slovenia, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Slovenian Research Agency, Ministry of Agriculture, Forestry and Food of the Republic of Slovenia V4-0324 BI-FR/07-08-INRA-003, INRA, Ministry of higher Education, Science and Technology (MESST), COST action 872, and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: Models, Molecular, 0106 biological sciences, Transcription, Genetic, Parasitism, Potato cyst nematode, Subspecies, 01 natural sciences, Host Specificity, GLOBODERA PALLIDA, Evolution, Molecular, 03 medical and health sciences, Botany, Genetics, medicine, Animals, Cyst, Tylenchoidea, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, Gene, Phylogeny, Solanaceae, Ecology, Evolution, Behavior and Systematics, Polysaccharide-Lyases, 030304 developmental biology, RELATION HOTE-PARASITE, 0303 health sciences, Polymorphism, Genetic, Models, Genetic, biology, Host (biology), Point mutation, Genetic Variation, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, Protein Structure, Tertiary, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Gene Components, Pectate lyase, Sequence Alignment, 010606 plant biology & botany
Abstract: Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; While pectate lyases are major parasitism factors in plant-parasitic nematodes, there is little information on the variability of these genes within species and their utility as pathotype or host range molecular markers. We have analysed polymorphisms of pectate lyase 2 (pel-2) gene, which degrades the unesterified polygalacturonate (pectate) of the host cell-wall, in the genus Globodera. Molecular variability of the pel-2 gene and the predicted protein was evaluated in populations of G. rostochiensis, G. pallida, G. "mexicana" and G. tabacum. Seventy eight pel-2 sequences were obtained and aligned. Point mutations were observed at 373 positions, 57% of these affect the coding part of the gene and produce 129 aa replacements. The observed polymorphism does not correlate either to the pathotypes proposed in potato cyst nematodes (PCN) or the subspecies described in tobacco cyst nematodes. The trees reveal a topology different from the admitted species topology as G. rostochiensis and G. pallida sequences are more similar to each other than to G. tabacum. Species-specific sites, potentially applicable for identification, and sites distinguishing PCN from tobacco cyst nematodes, were identified. As both G. rostochiensis and G. pallida display the same host range, but distinct from G. tabacum, which cannot parasitize potato plants, it is tempting to speculate that pel-2 genes polymorphism may be implicated in this adaptation, a view supported by the fact that no active pectate lyase 2 was found in G. "mexicana", a close relative of G. pallida that is unable to develop on cultivated potato varieties
Published: 2011

36. The Cyst Nematode SPRYSEC Protein RBP-1 Elicits Gpa2- and RanGAP2-Dependent Plant Cell Death

Author: Peter Moffett, Alexandra Blanchard, Melanie A. Sacco, Marianne J. Jaubert, Geert Smant, Aska Goverse, Kamila Koropacka, Eric Grenier, Boyce Thompson Institute [Ithaca], Laboratory of Nematology, Wageningen University and Research [Wageningen] (WUR), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Département de biologie [Sherbrooke] (UdeS), Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, GTPase-activating protein, [SDV]Life Sciences [q-bio], 01 natural sciences, pomme de terre, Biology (General), Globodera pallida, nb-lrr protein, avirulence genes, Peptide sequence, nématode, Plant Proteins, Genetics, globodera-pallida, 0303 health sciences, education.field_of_study, Cell Death, biology, EPS-2, GTPase-Activating Proteins, Helminth Proteins, gène de résistance, Potato virus X, protéine, sequence alignment, rich repeat protein, potato, Research Article, Plant Biology/Plant-Biotic Interactions, Hypersensitive response, endocrine system, globodera pallida, QH301-705.5, Recombinant Fusion Proteins, Molecular Sequence Data, Immunology, Population, Virulence, Molecular Biology/Molecular Evolution, Microbiology, 03 medical and health sciences, Virology, Tobacco, Hypersensitivity, Animals, Amino Acid Sequence, Tylenchoidea, Selection, Genetic, education, virus-resistance, Laboratorium voor Nematologie, Molecular Biology, 030304 developmental biology, downy mildew, éliciteur, fungi, RC581-607, biology.organism_classification, Fusion protein, Plant Leaves, Potexvirus, arabidopsis, solanum tuberosum, Amino Acid Substitution, Parasitology, Laboratory of Nematology, Immunologic diseases. Allergy, disease resistance genes, 010606 plant biology & botany
Abstract: Plant NB-LRR proteins confer robust protection against microbes and metazoan parasites by recognizing pathogen-derived avirulence (Avr) proteins that are delivered to the host cytoplasm. Microbial Avr proteins usually function as virulence factors in compatible interactions; however, little is known about the types of metazoan proteins recognized by NB-LRR proteins and their relationship with virulence. In this report, we demonstrate that the secreted protein RBP-1 from the potato cyst nematode Globodera pallida elicits defense responses, including cell death typical of a hypersensitive response (HR), through the NB-LRR protein Gpa2. Gp-Rbp-1 variants from G. pallida populations both virulent and avirulent to Gpa2 demonstrated a high degree of polymorphism, with positive selection detected at numerous sites. All Gp-RBP-1 protein variants from an avirulent population were recognized by Gpa2, whereas virulent populations possessed Gp-RBP-1 protein variants both recognized and non-recognized by Gpa2. Recognition of Gp-RBP-1 by Gpa2 correlated to a single amino acid polymorphism at position 187 in the Gp-RBP-1 SPRY domain. Gp-RBP-1 expressed from Potato virus X elicited Gpa2-mediated defenses that required Ran GTPase-activating protein 2 (RanGAP2), a protein known to interact with the Gpa2 N terminus. Tethering RanGAP2 and Gp-RBP-1 variants via fusion proteins resulted in an enhancement of Gpa2-mediated responses. However, activation of Gpa2 was still dependent on the recognition specificity conferred by amino acid 187 and the Gpa2 LRR domain. These results suggest a two-tiered process wherein RanGAP2 mediates an initial interaction with pathogen-delivered Gp-RBP-1 proteins but where the Gpa2 LRR determines which of these interactions will be productive., Author Summary Biotrophic plant pathogens produce effector proteins that are delivered to the host cytoplasm where they alter defense responses and metabolism to favor pathogen colonization. In turn, plants have evolved intra-cellular proteins to recognize pathogen effector proteins, known as NB-LRR proteins, which are similar in structure to animal NOD-LRR immune receptors. While effector proteins recognized by NB-LRR proteins have been identified from many organisms, the identification of such proteins from metazoan plant parasites has presented unique challenges due to the lack of genetically tractable model species. The potato Gpa2 protein confers resistance to some isolates of the potato pale cyst nematode, Globodera pallida. In this report, we show that Gpa2 recognizes certain variants of the G. pallida protein, Gp-RBP-1, which is highly polymorphic both within and between populations. This recognition in turn induces defense responses, including a form of programmed cell death characteristic of plant immune receptor activation. Moreover, we show that a Gpa2-interacting protein, RanGAP2, is required for Gpa2 function and that activation of Gpa2 is enhanced when Gp-RBP-1 is artificially tethered to RanGAP2. Thus, our findings suggest that RanGAP2 acts as a recognition co-factor for Gpa2, and have important implications for our understanding of the mechanisms and evolution of pathogen recognition by NB-LRR proteins.
Published: 2009

37. Host status and reaction of Medicago truncatula accessions to infection by three major pathogens of pea (Pisum sativum) and alfalfa (Medicago sativa)

Author: Anne Moussart, Bernard Tivoli, Angélique Lesné, Magali Esquibet, Caroline Onfroy, Eric Grenier, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, APHANOMYCES EUTEICHES, Plant Science, Horticulture, Plant disease resistance, 01 natural sciences, MYCOSPHAERELLA PINODES, 03 medical and health sciences, DITYLENCHUS DIPSACI, Sativum, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Medicago sativa, 030304 developmental biology, 0303 health sciences, biology, Ditylenchus dipsaci, fungi, food and beverages, biology.organism_classification, Ascochyta, Medicago truncatula, Aphanomyces euteiches, Mycosphaerella, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Ditylenchus dipsaci, the stem nematode of alfalfa (Medicago sativa), Mycosphaerella pinodes, cause of Ascochyta blight in pea (Pisum sativum) and Aphanomyces euteiches, cause of pea root rot, result in major yield losses in French alfalfa and pea crops. These diseases are difficult to control and the partial resistances currently available are not effective enough. Medicago truncatula, the barrel medic, is the legume model for genetic studies, which should lead to the identification and characterization of new resistance genes for pathogens. We evaluated a collection of 34 accessions of M. truncatula and nine accessions from three other species (two from M. italica, six from M. littoralis and one from M. polymorpha) for resistance to these three major diseases. We developed screening tests, including standard host references, for each pathogen. Most of the accessions tested were resistant to D. dipsaci, with only three accessions classified as susceptible. A very high level of resistance to M. pinodes was observed among the accessions, none of which was susceptible to this pathogen. Conversely, a high level of variation, from resistant to susceptible accessions, was identified in response to infection by A. euteiches
Published: 2007

38. Sequence Polymorphism of 2 Pioneer Genes Expressed in Phytoparasitic Nematodes Showing Different Host Ranges

Author: Didier Fouville, Alexandra Blanchard, Magali Esquibet, Eric Grenier, Didier Mugniery, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Nonsynonymous substitution, Male, Nematoda, Transcription, Genetic, Molecular Sequence Data, medicine.disease_cause, 01 natural sciences, NEMATODE A KYSTE, 03 medical and health sciences, Genetics, medicine, Animals, Amino Acid Sequence, RNA, Messenger, Globodera pallida, Molecular Biology, Gene, Genetics (clinical), Conserved Sequence, Crosses, Genetic, In Situ Hybridization, 030304 developmental biology, Hybrid, Plant Diseases, RELATION HOTE-PARASITE, chemistry.chemical_classification, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Polymorphism, Genetic, Stichodactyla helianthus, biology, Sequence Homology, Amino Acid, Toxin, Host (biology), Plants, biology.organism_classification, PATHOGENECITE, Amino acid, chemistry, Female, Sequence Alignment, 010606 plant biology & botany, Biotechnology
Abstract: International audience; In order to identify genes involved in pathogenicity, we compared the closely related species Globodera pallida (GP) and Globodera "mexicana" (GM) that have different host ranges and are able to produce viable and fertile hybrids. Three pioneer genes were previously identified as differentially expressed between GP and GM: GPLIA7 and GPLIB3 were found to be more highly expressed in GP, whereas GMLIVG9 was found more highly expressed in GM. In this study, we showed that Ia7 and IVg9 genes probably encode products secreted by the subventral oesophageal glands and the dorsal oesophageal gland, respectively. No Blast homolog was found in the databases, but a metridin-like ShK (Stichodactyla helianthus) toxin domain was identified in the Ia7 sequence. Analysis of the full-length sequences of these 2 genes between GP and GM revealed a high level of interspecies variability (8% for the Ia7 transcript and 17% for the IVg9 transcript) and a high proportion (90%) of nonsynonymous mutations among the substitutions observed. This suggested that these 2 pioneer genes are under strong diversifying selection pressures and therefore may be involved in pathogenicity. Further investigations of the sequence polymorphism of Ia7 and IVg9 genes were conducted in GP x GM hybrid lines that were selected in laboratory conditions for their different ability to develop on potato and black nightshade. As similar sequences were obtained for all the hybrid lines tested independently of their pathogenicity status, no correlation could be established between IA7 and IVG9 amino acid changes and the host range differences observed between GP and GM
Published: 2007

39. Intra-species DNA polymorphism in the tobacco cystnematode complex (Globoderatabacum) using AFLP

Author: Laurent Marché, Didier Mugniery, Eric Grenier, Sylvie Valette, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, UE FAIR PL95_0896, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut de Génétique, Environnement et Protection des Plantes (IGEPP)
Subjects: 0106 biological sciences, Nematoda, [SDV]Life Sciences [q-bio], markers, 01 natural sciences, 03 medical and health sciences, Tobacco, Botany, geographic distribution, distribution, Genetics, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cyst, Genetic variability, Globodera tabacum, Molecular Biology, Phylogeny, 030304 developmental biology, geographic, 0303 health sciences, Polymorphism, Genetic, biology, Heteroderinae, fungi, Dna polymorphism, Marché, food and beverages, marqueurs, General Medicine, genetic diversity, biology.organism_classification, medicine.disease, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Nematode, classification, diversité génétique, Amplified fragment length polymorphism, Polymorphism, Restriction Fragment Length, distribution géographique, 010606 plant biology & botany, Biotechnology
Abstract: Amplified fragment length polymorphism (AFLP) was used to obtain information on the within-species geneticvariability of the tobacco cyst – nematode (TCN) complex. AFLP was found to be well suited to this type ofstudy. The current classification of TCN was confirmed. Results indicate that the Globodera tabacum solanacearumgroup, believed to be restricted to the U.S.A., also occurs in Mexico. The within-species variability of TCN is considerable.Populations from Mexico may form a new subgroup. AFLP group-specific markers were identified for two ofthe TCN subgroups: Globodera tabacum tabacum and Globodera tabacum solanacearum.; La technique dite de l'AFLP a été utilisée sur les nématodes à kystes du tabac (TCN) afin d'acquérir des connaissances sur leur polymorphisme moléculaire intra-spécifique. L'efficience de la technique AFLP pour ce type d'études a été réaffirmée. La classification intra-spécifique des TCN communément admise est confirmée. Les résultats indiquent que le groupe Globodera tabacum solanacearum, jusqu'à présent décrit uniquement aux États-Unis, existe également au Mexique. Une variabilité intra-spécifique élargie est mise en évidence au sein des TCN. Des populations originaires du Mexique pourraient former un nouveau sous-groupe. Des marqueurs AFLP spécifiques pour deux des sous-groupes du complexe des TCN, Globodera tabacum tabacum et Globodera tabacum solanacearum, sont mis en évidence.Mots clés : Heteroderinae, classification, marqueurs, diversité génétique, distribution géographique.
Published: 2001

40. Genome sizes of the entomopathogenic nematodes Steinernema carpocapsae and Heterorhabditis bacteriophora (Nematoda : Rhabditida)

Author: Eric Grenier, Pierre Abad, François Catzeflis, Laboratoire de biologie des invertébrés, Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: [SDV]Life Sciences [q-bio], 030303 biophysics, Genome, Microbiology, 03 medical and health sciences, Cot analysis, Botany, Animals, Parasite hosting, Repeated sequence, Genome size, ComputingMilieux_MISCELLANEOUS, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, 0303 health sciences, biology, DNA, Helminth, Heterorhabditis, biology.organism_classification, Molecular Weight, [SDV] Life Sciences [q-bio], Kinetics, Infectious Diseases, Heterorhabditis bacteriophora, Nucleic Acid Renaturation, Animal Science and Zoology, Parasitology, Rhabditoidea, Rhabditida
Abstract: There is currently no information on the genome size and complexity in the entomoparasitic nematodes Steinernema and Heterorhabditis. DNA reassociation kinetics were used to determine the genome size and complexity in 2 species: Steinernema carpocapsae and Heterorhabditis bacteriophora. C0t curves derived from renaturation kinetics of denatured DNA indicate that the genomes of these entomoparasitic rhabditids are different both in size and complexity. Genome sizes were estimated at 2·3 × 108 bp for S. carpocapsae and 3·9 × 107 bp for H. bacteriophora and repetitive DNA contents were found to represent 39% and 51% of these respective genomes.
Published: 1997

41. Satellite DNA sequences as taxonomic markers in nematodes of agronomic interest

Author: Eric Grenier, Pierre Abad, Philippe Castagnone-Sereno, Laboratoire de biologie des invertébrés, Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: 0106 biological sciences, 0303 health sciences, Ecology, Satellite DNA, [SDV]Life Sciences [q-bio], fungi, Biological pest control, Interspecific competition, Biology, Heterorhabditis, biology.organism_classification, 01 natural sciences, Intraspecific competition, Crop protection, [SDV] Life Sciences [q-bio], 03 medical and health sciences, Nematode, Evolutionary biology, Parasitology, Taxonomy (biology), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany
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.
Published: 1997

42. Molecular characterization of two species-specific tandemly repeated DNAs from entomopathogenic nematodes Steinernema and Heterorhabditis (Nematoda : Rhabditida)

Author: Christian Laumond, Eric Grenier, Pierre Abad, Laboratoire de biologie des invertébrés, Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: 0106 biological sciences, Insecta, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, DNA, Satellite, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, chemistry.chemical_compound, Species Specificity, Sequence Homology, Nucleic Acid, Consensus sequence, Animals, Cloning, Molecular, Pest Control, Biological, Molecular Biology, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Repetitive Sequences, Nucleic Acid, Genetics, 0303 health sciences, Base Sequence, Entomopathogenic nematode, Sequence Analysis, DNA, Heterorhabditis, DNA, Helminth, biology.organism_classification, [SDV] Life Sciences [q-bio], chemistry, Steinernema glaseri, Heterorhabditis bacteriophora, Parasitology, Rhabditoidea, Rhabditida, DNA
Abstract: Two AluI tandemly repeated DNAs were cloned from two entomopathogenic nematodes: the first one from Steinernema glaseri and the second one from Heterorhabditis bacteriophora. The monomeric units of these two satellite DNAs have a repeat length of 174 and 168 bp, respectively. These AluI repeated element families appear to constitute 5.5% of the S. glaseri genome and 5% of the H. bacteriophora genome. Their A + T contents were estimated at 55% and 57%. Moreover, the monomers of these two families are quite homogeneous in sequence, showing, on average, 3.9% and 2.7% divergence from their respective consensus sequence. These results suggest that some mechanism is acting to maintain the homogeneity of these repeated DNAs despite their abundance. We have also shown that these two DNA families are species-specific and therefore could be used for the identification of Steinernema and Heterorhabditis entomopathogenic nematode species.
Published: 1996

43. What determines host specificity in hyperspecialized plant parasitic nematodes?

Author: Michael Sabeh, Etienne Lord, Éric Grenier, Marc St-Arnaud, and Benjamin Mimee
Subjects: Plant-parasitic nematode, Globodera, Transcriptomic study, RNA-seq, Pathogenicity, Effectors, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background In hyperspecialized parasites, the ability to grow on a particular host relies on specific virulence factors called effectors. These excreted proteins are involved in the molecular mechanisms of parasitism and distinguish virulent pathogens from non-virulent related species. The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida are major plant-parasitic nematodes developing on numerous solanaceous species including potato. Their close relatives, G. tabacum and G. mexicana are stimulated by potato root diffusate but unable to establish a feeding site on this plant host. Results RNA sequencing was used to characterize transcriptomic differences among these four Globodera species and to identify genes associated with host specificity. We identified seven transcripts that were unique to PCN species, including a protein involved in ubiquitination. We also found 545 genes that were differentially expressed between PCN and non-PCN species, including 78 genes coding for effector proteins, which represent more than a 6-fold enrichment compared to the whole transcriptome. Gene polymorphism analysis identified 359 homozygous non-synonymous variants showing a strong evidence for selection in PCN species. Conclusions Overall, we demonstrated that the determinant of host specificity resides in the regulation of essential effector gene expression that could be under the control of a single or of very few regulatory genes. Such genes are therefore promising targets for the development of novel and more sustainable resistances against potato cyst nematodes.
Published: 2019
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44. Host status and reaction of Medicago truncatula accessions to infection by three major pathogens of pea (Pisum sativum) and alfalfa (Medicago sativa).

Author: Magali Esquibet, Eric Grenier, and Bernard Tivoli
Published: 2007

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