Author: "Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)" - Searchworks@Jio Institute Digital Library Search Results

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Start Over Author "Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)"

164 results on '"Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)"'

1. 'Plantas que toda la vida han estado': una co-investigación alrededor de la cocina y las relaciones bioculturales asociadas a plantas alimenticias locales en la ruralidad de Bogotá

Author: Consuegra, Cristina, Ortiz, Stefan, Cely Santos, Marcela, Van der Hammen, María Clara, Pérez, Darío, Leuphana Universität Lüneburg, Universidad Nacional de Colombia [Bogotà] (UNAL), Rachel Carson Centre, Partenaires INRAE, Universidad Externado de Colombia, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Sorbonne Université (SU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)
Subjects: [SDE.ES]Environmental Sciences/Environmental and Society, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SHS]Humanities and Social Sciences
Abstract: International audience; A process of co-research with farmers in the rural area of Bogotá, documented traditional culinary practices and held meetings to discuss their territorial implications and the challenges of their transformations. The dialogues promoted the reactivation of memories and perceptions, linking the space of kitchens and territories, and included conversations on the risks and opportunities of innovations triggered by urban-rural relations. This research sheds light on the persistence of linkages related to local biodiversity, which represent a key asset for the conservation of biocultural diversity and of the material and immaterial heritage of Bogota.; A través de un proceso de co-investigación con sabedores de la ruralidad bogotana, se documentaron prácticas culinarias tradicionales y se realizaron encuentros para conversar sobre sus implicaciones territoriales y los desafíos de sus transformaciones. El diálogo permitió reactivar la memoria y las percepciones que, desde la cocina, remiten al territorio, y conversar sobre los riesgos y potencialidades de las innovaciones en las prácticas suscitadas, considerando la porosidad de las fronteras urbano-rurales. Se evidencia una persistencia de conocimientos y relaciones con la biodiversidad local, que representan un acervo esencial para pensar la conservación y dinamización de la diversidad biocultural y su integración como parte del patrimonio cultural material e inmaterial de Bogotá.
Published: 2021

2. Innovative teaching approaches in applied plant sciences: experiences from European universities within the ESCAPAdE network

Author: Rose, Julien, Polesny, Zbynek, Ballini, Elsa, Tixier, Marie-Stéphane, This, Dominique, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Czech University of Life Sciences Prague (CZU), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, European Project: 048110,2018-1-FR01-KA203-048110,ESCAPAdE(2018), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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 Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Teaching Methods, [SHS.EDU]Humanities and Social Sciences/Education, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Innovation pédagogique, Innovative approach, Applied plant sciences
Published: 2021

3. El trabajo comunitario en la conservación de la biodiversidad en la Reserva Natural de la Sociedad Civil Agua Clara-Valle Lindo

Author: Lòpez, Jorge-Hernán, Pérez, Darío, Fundacion Ecologica Reserva Las Mellizas, Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad Nacional de Colombia [Bogotà] (UNAL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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: [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDE.ES]Environmental Sciences/Environmental and Society, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

4. La conservación por cuenta propia, el caso de la Reserva Natural Suma-Paz

Author: Ruiz, Manuela, Pérez, Darío, Asociacion Reserva Natural Suma Paz, Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Universidad Nacional de Colombia [Bogotà] (UNAL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, [SDE.ES]Environmental Sciences/Environmental and Society, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

5. El Qhapaq Ñan y el patrimonio biocultural de los Andes

Author: Afanador, Claudia, Sánchez-Delgado, Gerardo, Pérez, Darío, Universidad de nariño, Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad Nacional de Colombia [Bogotà] (UNAL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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: [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDE.ES]Environmental Sciences/Environmental and Society, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

6. La búsqueda de la Zona de Reserva Campesina de Sumapaz

Author: Pérez, Darío, Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Universidad Nacional de Colombia [Bogotà] (UNAL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDE.ES]Environmental Sciences/Environmental and Society, ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract: International audience
Published: 2019

7. Conservación de la diversidad de yuca en los sistemas tradicionales de cultivo de la Amazonía

Author: Pérez, Darío, Mora, Rubén, López Carrascal, Camilo, Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Universidad Nacional de Colombia [Bogotà] (UNAL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: cultural identity, identidad cultural, población indígena, food security, [SDE.ES]Environmental Sciences/Environmental and Society, [SHS]Humanities and Social Sciences, Agrobiodiversity, Agrobiodiversidad, ethnobotany, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, seguridad alimentaria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, indigenous peoples, etnobotánica
Abstract: International audience; Cassava is crucial for the food security of hundreds of millions of people around the world. Even though the main source of propagation of the crop is through asexual seed by stakes (stems-cuttings) a relative high intraspecific diversity has been identified, mainly in the traditionally managed cultivation systems. Some studies on the diversity of cassava, based on molecular and morphological markers, are documented focusing on those made in the Amazon in this review. Also, the main factors that have determined the use and conservation of this diversity are exposed, such as the spontaneous appearance of seeds of sexual origin, the system of indigenous chagras, the biocultural memory and the ease of seed exchange between communities. From this perspective, it is evident that in traditional management systems the conservation and use of intraspecific diversity is a priority element that has been lost in large-scale farming systems. In traditional management systems, there is an ethnobotanical link that survives and invites us to seek alternative practices that ensure the maintenance of diversity, allowing efficient productivity and even better management to reduce the risk of incidence of some pests and diseases.; La yuca es determinante para la seguridad alimentaria de cientos de millones de personas alrededor del mundo. A pesar de que el principal medio de propagación del cultivo es a través de semilla asexual por estacas (tallos maduros) se ha revelado una relativamente alta diversidad intraespecífica, principalmente en los sistemas de cultivo de manejo tradicional. En esta revisión se documentan algunos estudios realizados sobre la diversidad de la yuca, tanto por marcadores moleculares como morfológicos, centrándose en aquellos realizados en el Amazonas. También se exponen los principales factores que han determinado el aprovechamiento y conservación de esta diversidad, tales como la aparición espontánea de semillas de origen sexual, el sistema de chagras indígenas, la memoria biocultural y la facilidad de intercambio de semilla entre comunidades. Finalmente, se pone de manifiesto que en los sistemas de manejo tradicional la conservación y uso de la diversidad intraespecífica se constituye en un elemento prioritario que se ha perdido en los sistemas de cultivo a gran escala. En los sistemas de manejo tradicional existe un vínculo etnobotánico que pervive e invita a buscar prácticas alternativas que aseguran un mantenimiento de la diversidad, permitiendo una productividad eficiente e incluso se hace un mejor manejo para disminuir los riesgos de incidencia de algunas plagas y enfermedades.
Published: 2019

8. La topofilia en la construcción de procesos de Educación Ambiental Comunitarios en Colombia

Author: Pérez, Darío, Patrimoines locaux, Environnement et Globalisation (PALOC), Sorbonne Université (SU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Universidad Nacional de Colombia [Bogotà] (UNAL), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: territorial appropriation, [SHS.EDU]Humanities and Social Sciences/Education, conservation, space, conservación, [SHS.GEO]Humanities and Social Sciences/Geography, [SDE.ES]Environmental Sciences/Environmental and Society, espaciante, problemas ambientales, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, environmental issues, patrimonio biocultural, biocultural heritage, apropiación territorial
Abstract: International audience; In Colombia, despite the efforts to create Environmental Education processes that have an impact on the needs of the territory and which are relevant for the different generations, there are still no strong government programs on the subject that, with solid variables, measure the impact of these processes in society; on the contrary, nowadays there are short-term projects seeking to meet institutional requirements.This text suggests the use of topophilia as a link between individuals and the place, conceived as a strategy for territorial appropriation and as the first step to achieve a community environmental education that shapes spatial and democratic people who are conscious of their role in the formulation of plans for the management and conservation of local biodiversity, as a biocultural and self-defining heritage.; En Colombia, pese a los esfuerzos por generar procesos de Educación Ambiental de impactoen las necesidades del territorio y de trascendencia a través de las generaciones, aún noexisten programas gubernamentales fuertes en la materia y que, con variables sólidas, midanel impacto de estos procesos en la sociedad; por el contrario, hoy en día se formulan proyectoscortoplacistas que buscan responder a los requerimientos institucionales.En este texto se sugiere el uso de la topofilia, vista como el vínculo que tienen los sujetos conel lugar, como una estrategia para la apropiación territorial y como el primer paso para lograruna educación ambiental comunitaria que forme sujetos espaciantes, democráticos yconscientes de su papel en la formulación de planes de manejo y conservación de labiodiversidad local, como patrimonio biocultural e identitario
Published: 2017

9. [Use of plants by farming communities in rural areas of Bogotá D.C., Colombia]

Author: Pérez, Darío, Matiz-Guerra, Laura Catalina, Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Universidad Nacional de Colombia [Bogotà] (UNAL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Ethnobotany, Local agrobiodiversity, home gardens, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDE.ES]Environmental Sciences/Environmental and Society, paisaje biocultural, [SHS]Humanities and Social Sciences, ethnobotany, biocultural landscape, Biocultural landscape, Etnobotánica, huertas campesinas, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Home gardens, etnobotánica, Agrobiodiversidad local
Abstract: International audience; Colombian farmers possess valuable ethnobotanical knowledge that forms part of their identity andbiocultural heritage and is at risk of disappearing as a result of changesin land use, internal migrations and market dynamics. This study documents the uses of plants by farming communities living in rural areas of Bogotá, D.C. Qualitative research methods includinginterviews andethnobotanical walks were applied during visits to the use areas of 18 key informants who provided information about 231 species of useful plants associated with 320 common names. These species correspond to 86 botanical families and 191 genera. The families Asteraceae (11%) and Lamiaceae (6%) were the ones with the highest percentage of species. Twelve use categories were determined, with medicinal uses predominating (39%). Relative value categorization indicates that varieties of “Cubio” (Tropaeolum tuberosum) are defined as very important, while “Encenillo” (Weinmannia tomentosa) from surrounding wooded areas, had the greatest number of uses reported (five). Among the useful species reported, 58% are sown in home gardens, while 42% are wild species. Thus, in the rural areas of Bogota home gardens, together with the adjacent wild vegetation play a fundamental role in subsistence and maintenance of the local agrobiodiversity, suggesting the importance of the valuation and integration of farmers’ knowledge in management plans and biodiversity conservation inhigh-Andean ecosystems.; Los campesinos colombianos poseen un valioso conocimiento etnobotánico que constituye parte del patrimonio biocultural e identitario que está en riesgo de desaparecer, producto del cambio en el uso de suelo, migraciones internas y dinámicas del mercado. En este estudio se documentaron usos de las plantas por parte de comunidades campesinas que viven en las áreas rurales de la ciudad de Bogotá. Basados en métodos de investigación cualitativa aplicados en entrevistas y en caminatas etnobotánicas se visitaron las áreas de aprovechamiento de 18 sabedores quienes proporcionaron información de 231 especies de plantas útiles asociadas a 320 nombres comunes. Estas especies corresponden a 86 familias botánicas y 191 géneros. Las familias Asteraceae (11%) y Lamiaceae (6%) son las que presentan mayor porcentaje de especies. Se determinaron 12 categorías de uso, dentro de las que predominó el uso medicinal (39%). La categorización de valor relativo indica que las variedades de “Cubio” (Tropaeolum tuberosum) están definidas como muy importantes, mientras que el “Encenillo” (Weinmannia tomentosa), proveniente de áreas boscosas circundantes, con cinco usos reportados, fue el que mayor número de registros presentó. Entre las especies útiles reportadas el 58% son sembradas en las huertas, mientras que el 42% son especies silvestres. En ese sentido en la ruralidad de Bogotá las huertas campesinas junto con la vegetación silvestre adyacente cumplen un papel fundamental para el autoconsumo y el mantenimiento de la agrobiodiversidad local, sugiriendo la importancia de la valoración y la integración de los conocimientos campesinos en planes de manejo y conservación de la biodiversidad de los ecosistemas altoandinos.
Published: 2017

10. A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown

Author: Axelle Andrieux, Pascal Frey, Clémentine Louet, Fabien Halkett, Mathilde Gorse, Bénédicte Fabre, Sébastien Duplessis, Jérémy Pétrowski, Antoine Persoons, Stéphane De Mita, Méline Saubin, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), ANR-17-CE32-0010,WABSARF,Adaptation intraspécifique et interspécifique des champignons responsables des rouilles(2017), ANR-18-CE32-0001,Clonix2D,Les conséquences génétiques de reproduction partiellement clonale dans les populations colonisant de nouveaux territoires(2018), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, biology, molecular evolution, food and beverages, Population genetics, Locus (genetics), Melampsora, gene-for-gene interaction, biology.organism_classification, 01 natural sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 03 medical and health sciences, effector, Molecular evolution, Genetic variation, Genotype, fungal pathogen, Allele, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; The deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R-mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici-populina is a damaging pathogen of poplars in Europe. It underwent a major adaptive event in 1994, with the breakdown of the poplar RMlp7 resistance gene. Population genomics studies identified a locus in the genome of M. larici-populina that probably corresponds to the candidate avirulence gene AvrMlp7. Here, to further characterize this effector, we used a population genetics approach on a comprehensive set of 281 individuals recovered throughout a 28-year period encompassing the resistance breakdown event. Using two dedicated molecular tools, genotyping at the candidate locus highlighted two different alterations of a predominant allele found mainly before the resistance breakdown: a nonsynonymous mutation and a complete deletion of this locus. This results in six diploid genotypes: three genotypes related to the avirulent phenotype and three related to the virulent phenotype. The temporal survey of the candidate locus revealed that both alterations were found in association during the resistance breakdown event. They pre-existed before the breakdown in a heterozygous state with the predominant allele cited above. Altogether, these results suggest that the association of both alterations at the candidate locus AvrMlp7 drove the poplar rust adaptation to RMlp7-mediated immunity. This study demonstrates for the first time a case of adaptation from standing genetic variation in rust fungi during a qualitative resistance breakdown.
Published: 2021

11. Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant–Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient

Author: Cheikh Ndiaye, Diégane Diouf, Fatoumata Fall, Dioumacor Fall, Estelle Tournier, Niokhor Bakhoum, Hervé Sanguin, Amadou Moustapha Bâ, Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE), Institut de Recherche pour le Développement (IRD), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Université du Sine Saloum El-Hadj Ibrahima NIASS (USSEIN), and Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM)
Subjects: 0106 biological sciences, Salinity, Cebinae, Arbuscular mycorrhizal fungi, 01 natural sciences, Interactions biologiques, Soil, Prosopis, Mycorrhizae, Tolérance au sel, Colonization, Soil Microbiology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, 0303 health sciences, Rhizosphere, Ecology, biology, Illumina sequencing, food and beverages, Vegetation, Plants, Communauté végétale, F40 - Écologie végétale, F60 - Physiologie et biochimie végétale, Relation plante sol, Soil Science, Poaceae, Intraspecific competition, 03 medical and health sciences, Glomeraceae, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arbuscular mycorrhiza [EN], Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Environmental gradient, Prosopis juliflora, 15. Life on land, biology.organism_classification, Sol salin, Plant-plant interactions, Species richness, 010606 plant biology & botany
Abstract: International audience; The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus-mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese's lands.
Published: 2021

12. Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments

Author: Olivier Maurin, Yohan Pillon, William J. Baker, Zachary S. Rogers, Helen C. F. Hopkins, Niroshini Epitawalage, Jason C. Bradford, Félix Forest, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Royal Botanic Gardens, Kew, College of Forestry [Corvallis], Oregon State University (OSU), New Mexico State University, Calleva Foundation, Sackler Trust, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 Royal Botanic Gardens [Kew]
Subjects: 0106 biological sciences, Paraphyly, Elaeocarpaceae, Biogeography, Antarctica, Australia, Caldcluvia, Gondwana, Madagascar, relicts, Weinmannia, Plant Science, Tribe (biology), 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Cunoniaceae, Genetics, Vicariance, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecology, Evolution, Behavior and Systematics, Research Articles, 030304 developmental biology, 0303 health sciences, biology, Invited Special Article, 15. Life on land, biology.organism_classification, Taxon, Evolutionary biology, Research Article
Abstract: PREMISE: Cunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long- range disjunctions. METHODS: We performed a phylogenomic study using the universal Angiosperms353 probe set for targeted sequence capture. We sampled 37 species covering all genera in the Cunoniaceae, and those in the three closely related families of the crown Oxalidales (Brunelliaceae, Cephalotaceae, and Elaeocarpaceae). We also performed analyses for molecular dating and ancestral area reconstruction. RESULTS: We recovered the topology (Cunoniaceae, (Cephalotaceae, (Brunelliaceae, Elaeocarpaceae))) and a well- resolved genus- level phylogeny of Cunoniaceae with strongly supported clades corresponding to all previously recognized tribes. As previously suspected, the genera Ackama and Weinmannia were recovered as paraphyletic. Australasia was inferred as the likely ancestral area for the family. CONCLUSIONS: The current distribution of Cunoniaceae is best explained by long-distance dispersal with a few possible cases of Australasian–American vicariance events. Extinctions may have been important in determining the mostly Oceanian distribution of this family while some genera in the tribe Cunonieae and in New Caledonia have undergone recent bursts of diversification. New generic diagnoses, 80 new combinations, and one new name are provided for a recircumscribed Ackama (including Spiraeopsis), a much smaller Weinmannia (mostly New World), and a resurrected Pterophylla to accommodate Old World taxa previously in Weinmannia, Note on uploaded file: 5_Cunoniaceae_14gene_dating.tar.gz is the Concatenated matrix of the 14 genes selected using Sortadate for the estimation of divergence times in Cunoniaceae
Published: 2021

13. Occurrence data for the two cryptic species of Cacopsylla pruni (Hemiptera: Psylloidea)

Author: Nicolas Sauvion, Jean Peccoud, Christine Meynard, David Ouvrard, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), This data paper was conceived within the stimulating framework of the KIM RIVE (Key Initiative Montpellier: Infectious Risks and Vectors, https://muse.edu.umontpellier.fr/key-initiatives-muse/rive), supported by MUSE (Montpellier University of Excellence, https://muse.edu.umontpellier.fr/en/muse-i-site) and the RIVOC key challenge (https://muse.edu.umontpellier.fr/2021/04/19/appel-a-projets-rivoc), supported by the Occitanie Region (France). Part of this work benefitted from a postdoctoral grant to NS funded by an INRA-CIRAD SDIPS grant (Speciation and Molecular Diagnosis of Insect Pest Species Complexes).. Field and molecular work for this study were supported by several projects during 15 years:- ECOGER 'Ecologie et adaptation des insectes phytophages en gestion de leurs populations' founded by 'Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation', France, SEE-ERANET, network 'Phytoplasma epidemiology', funded by the 6th EUFramework Programme for Research and Development (ERA-CT-2004-515805), SPEED@ID 'Accurate SPEciEs Delimitation and IDentification of Eukaryotic biodiversity using DNA markers'. A project proposed by F-BoL, the French Barcode of Life initative - Genoscope Evry-France, PRIMA PHACIE 'Pest risk assessment for the European Community plant health: A comparative approach with case studies', founded by European Food Safety Authority (EFSA), grant agreement CFP⁄EFSA⁄PLH, Bilateral project PIA BOSPHORUS between TUBITAK-Turkey and le Ministère des Affaires étrangères-France 'Role of the vectors (psyllids) in the dissemination of the diseases due to phytoplasma on fruit trees', PHYLOPSYL from the project 'Bibliothèque du vivant' (BdV) funded by three French institutions (the CNRS, INRA and MNHN), E-SPACE project number 1504-004, Improving epidemiosurveillance of Mediterranean and tropical plant diseases, French Agropolis Foundation., European Project, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Laboratoire de la santé des végétaux (LSV), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), INRA-CIRAD SDIPS grant (Speciation and molecular Diagnosis of Insect Pest Species complexes)2005-07: ECOGER 'Ecologie et adaptation des insectes phytophages en gestion de leurs populations' founded by le Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation-France, 2007-08: SEE-ERA.NET, network 'Phytoplasma epidemiology', funded by the 6th EU Frame-work Programme for Research and Development (contract number ERACT- 2004-515805)2009-11: SDIPS 'Mechanisms of Speciation & Molecular Diagnosis of Insect Pest Species complexes' founded by INRA-France, 2010-12: SPEED@ID 'Accurate SPEciEs Delimitation and IDentification of Eukaryotic biodiversity using DNA markers'. A project proposed by F-BoL, the French Barcode of Life initative - Genoscope Evry-France, 2010-12: PRIMA PHACIE 'Pest risk assessment for the European Community plant health: A comparative approach with case studies', founded by European Food Safety Authority (EFSA), grant agreement CFP⁄EFSA⁄PLH⁄2009⁄01, 2010-12: Bilateral project PIA BOSPHORUS between TUBITAK-Turkey and le Ministère des Affaires étrangères-France 'Role of the vectors (psyllids) in the dissemination of the diseases due to phytoplasma on fruit trees', 2011-13: PHYLOPSYL from the project 'Bibliothèque du vivant' (BdV) funded by three French institutions (the CNRS, INRA and MNHN), and 2015-2018: E-SPACE project number 1504-004, Improving epidemiosurveillance of Mediterranean and tropical plant diseases, French Agropolis Foundation.
Subjects: Asia, Insecta, Arthropoda, Cacopsylla pruni, QH301-705.5, Biodiversity & Conservation, Cacopsylla, Evolutionary biology, Horticulture, European stone fruit yellows, vector-borne plant pathogen, Hemiptera, Data analysis & Modelling, Sternorrhyncha, Systematics, Agricultural ecology, Ecology & Environmental sciences, Animalia, phytoplasma, Biology (General), 'Candidatus phytoplasma prunorum', Data Paper (Biosciences), Diseases & Pests, Biota, Psylloidea, psyllid, Europe, ' Candidatus phytoplasma prunorum', [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Psyllidae, Biogeography, Zoology & Animal Biology, Africa, species distribution, epidemiology, vecto, Americas, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Cacopsylla pruniisa psyllid that has been known since 1998 as the vector of the bacterium ‘Candidatus Phytoplasma prunorum’, responsible for the European stone fruit yellows (ESFY), a disease that affects species of Prunus. This disease is one of the major limiting factors for the production of stone fruits, most notably apricot (Prunus armeniaca) and Japanese plum (P. salicina), in all EU stone fruit-growing areas. The psyllid vector is widespread in the Western Palearctic, and evidence for the presence of the phytoplasma that it transmits to species of Prunus has been found in 15 of the 27 EU countries. Recent studies showed that C. pruni is actually composed of two cryptic species, which can be differentiated bymolecular markers. A literature review on the distribution of C. pruni was published in 2012, but it only provided presence or absence information at the country level and without distinction between the two cryptic species. Since 2012, numerous new records of the vector in several European countries have been published. We ourselves have acquired a large amountof data from sampling in France and other European countries. We have also carried out a thorough systematic literature review to find additional records, including all the original sources mentioningC. pruni (or its synonyms) since the first description by Scopoli in 1763. Our aim was to create an exhaustive georeferenced occurrence catalog, in particular in countries that are occasionnaly mentioned in the literature with little detail. Finally, for countries that seem suitable for the proliferation of C. pruni (USA, Canada, Japan, China, etc.), we digged deeper into the literature and reliablesources (e.g. checklist)to better subtanciateits current absence from those regions. Information on the distribution ranges of these vector psyllids is of crucial interest in order to best predict the vulnerability of stone fruit producing countries to the ESFY threat in the foreseeable future. We give free access to a unique file of 1975 records of all occurrence data in our possession concerning C. pruni, which we have gathered through more than twenty years of sampling efforts in Europe or through intensive text mining. We have made every effort to retrieve the source information for the records extracted from litterature (1201 records). Thus, we always give the title of the original reference, together with the page(s) citing C. pruni and, if possible, the year of sampling. To makethe results of this survey publicly available, we give a URL to access the literature sources. In most cases, this link allows to freely download a PDFfile. We also give access to information extracted from GBIF (162 exploitable data points on 245 occurrences found in the database), which we thoroughly checked and often supplemented to make the information more easily exploitable. We give access to our own unpublished georeferenced and genotyped record from 612samples taken over the last 20 years in several European countries (Switzerland, Belgium, Netherlands, Spain, etc.). Theseinclude two countries (Portugal and North Macedonia) for which the presence of C. pruni had notbeen reported before.Asour specimens have been genotyped (74 sites with species A solely, 202 with species B solely, and 310 with species A+B), our new data enable a better view of the geographical distribution of the two species at the Palaearctic scale.
Published: 2021

14. Identification of type III effectors modulating the symbiotic properties of Bradyrhizobium vignae strain ORS3257 with various Vigna species

Author: Songwattana, Pongpan, Chaintreuil, Clémence, Wongdee, Jenjira, Teulet, Albin, Mbaye, Mamadou, Piromyou, Pongdet, Gully, Djamel, Fardoux, Joel, Zoumman, Alexandre Mahougnon Aurel, Camuel, Alicia, Tittabutr, Panlada, Teaumroong, Neung, Giraud, Eric, Suranaree University of Technology (SUT), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Ctr Rech Bel Air, Inst Senegalais Rech Agr, Inst Rech Dev,Lab Commun Microbiol, Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), ANR-16-CE20-0013,SymEffectors,Système de sécrétion de type 3 pour la symbiose fixatrice d'azote(2016), ANR-20-CE20-0012,ET-Nod,Effecteurs déclenchant la nodulation chez les légumineuses(2020), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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: [SDV]Life Sciences [q-bio], Science, food and beverages, Medicine, Plant sciences, Microbiology, Publisher Correction, Article
Abstract: International audience; The Bradyrhizobium vignae strain ORS3257 is an elite strain recommended for cowpea inoculation in Senegal. This strain was recently shown to establish symbioses on some Aeschynomene species using a cocktail of Type III effectors (T3Es) secreted by the T3SS machinery. In this study, using a collection of mutants in different T3Es genes, we sought to identify the effectors that modulate the symbiotic properties of ORS3257 in three Vigna species ( V. unguiculata , V. radiata and V. mungo ). While the T3SS had a positive impact on the symbiotic efficiency of the strain in V. unguiculata and V. mungo , it blocked symbiosis with V. radiata . The combination of effectors promoting nodulation in V. unguiculata and V. mungo differed, in both cases, NopT and NopAB were involved, suggesting they are key determinants for nodulation, and to a lesser extent, NopM1 and NopP1, which are additionally required for optimal symbiosis with V. mungo . In contrast, only one effector, NopP2, was identified as the cause of the incompatibility between ORS3257 and V. radiata . The identification of key effectors which promote symbiotic efficiency or render the interaction incompatible is important for the development of inoculation strategies to improve the growth of Vigna species cultivated in Africa and Asia.
Published: 2021

15. NSP2, a key symbiotic regulator in the spotlight

Author: Johan Quilbé, Jean-François Arrighi, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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, 0301 basic medicine, Arachis, Physiology, NSP2, Regulator, Plant Science, Computational biology, Biology, Plant Root Nodulation, 01 natural sciences, nitrogen, symbiosis, Legume, 03 medical and health sciences, 030104 developmental biology, Symbiosis, Key (cryptography), [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nodulation, peanut, signalling, 010606 plant biology & botany
Abstract: International audience; Legumes have the remarkable ability to develop root nodules with nitrogen-fixing rhizobial bacteria. This symbiosis enables them to overcome nitrogen limitation affecting their growth, and such a nutritional advantage is key to the ecological and agronomic success of legumes. Intriguingly, non-nodulating lines can be obtained through inbreeding work in cultivated peanut. Using elegant genetic approaches, Peng et al. (2021) have elucidated this 40-year-old mystery by identifying the underlying genes. They are the two homoeologs of the symbiotic signalling gene NSP2, pinpointing NSP2 as a gene of primary adaptative importance for nodulation in legumes.
Published: 2021

16. Tracing the Origin and Evolutionary History ofPyricularia oryzaeInfecting Maize and Barnyard Grass

Author: Adel Pordel, Mohammad Javan-Nikkhah, Florian Charriat, Pierre Gladieux, Sébastien Ravel, Henri Adreit, Ali Moumeni, Sandrine Cros-Arteil, Didier Tharreau, Joëlle Milazzo, Amir Mirzadi-Gohari, Agricultural Research, Education and Extension Organisation (AREEO ), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), University of Tehran, Rice Research Institute of Iran (RRII), High Council for Research of the University of Tehran, CIRAD Institute, ANR-18-CE20-0016,MagMAX,Structure, évolution et fonction d'effecteurs de virulence fongiques(2018), and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)
Subjects: 0106 biological sciences, Phylogénie, Pyricularia, Plant Science, Echinochloa, maize, 01 natural sciences, F30 - Génétique et amélioration des plantes, Setaria (graminée), blasts (of plants) [EN], Pyricularia oryzae, 2. Zero hunger, 0303 health sciences, food and beverages, Magnaporthe oryzae, pathogen detection, Génotype, Setaria, Triticum aestivum, blaste, host range, Oryza sativa, Relation hôte pathogène, Biology, Zea mays, Agent pathogène, host range [EN], Crop, 03 medical and health sciences, evolution, Lolium, genomics, new disease, H20 - Maladies des plantes, 030304 developmental biology, Host (biology), Maladie fongique, mergence, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Agronomy, Weed, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Blast disease is a notorious fungal disease leading to dramatic yield losses on major food crops such as rice and wheat. The causal agent, Pyricularia oryzae, encompasses different lineages, each having a different host range. Host shifts are suspected to have occurred in this species from Setaria spp. to rice and from Lolium spp. to wheat. The emergence of blast disease on maize in Iran was observed for the first time in the north of the country in 2012. We later identified blast disease in two additional regions of Iran: Gilan in 2013 and Golestan in 2016. Epidemics on the weed barnyard grass (Echinochloa spp.) were also observed in the same maize fields. Here, we showed that P. oryzae is the causal agent of this disease on both hosts. Pathogenicity assays in the greenhouse revealed that strains from maize can infect barnyard grass and conversely. However, genotyping with simple sequence repeat markers and comparative genomics showed that strains causing field epidemics on maize and on barnyard grass are different, although they belong to the same previously undescribed clade of P. oryzae. Phylogenetic analyses including these strains and a maize strain collected in Gabon in 1985 revealed two independent host-range expansion events from barnyard grass to maize. Comparative genomics between maize and barnyard grass strains revealed the presence or absence of five candidate genes associated with host specificity on maize, with the deletion of a small genomic region possibly responsible for adaptation to maize. This recent emergence of P. oryzae on maize provides a case study to understand host range expansion. Epidemics on maize raise concerns about potential yield losses on this crop in Iran and potential geographic expansion of the disease.
Published: 2021

17. RibBX of Bradyrhizobium ORS285 Plays an Important Role in Intracellular Persistence in Various Aeschynomene Host Plants

Author: Nouwen, Nico, Arrighi, Jean-François, Gully, Djamel, Giraud, Eric, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), ANR-16-CE20-0013,SymEffectors,Système de sécrétion de type 3 pour la symbiose fixatrice d'azote(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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: nodule organogenesis, vitamin B2, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, mutualism, Botany, food and beverages, rhizobium-legume symbiosis, Microbiology, QR1-502, rhizobium, QK1-989, bacteria-plant symbiosis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Abstract: International audience; Bradyrhizobium ORS285 forms a nitrogen-fixating symbiosis with both Nod factor (NF)-dependent and NF-independent Aeschynomene spp. The Bradyrhizobium ORS285 ribBA gene encodes for a putative bifunctional enzyme with 3,4-dihydroxybutanone phosphate (3,4-DHBP) synthase and guanosine triphosphate (GTP) cyclohydrolase II activities, catalyzing the initial steps in the riboflavin biosynthesis pathway. In this study, we show that inactivating the ribBA gene does not cause riboflavin auxotrophy under free-living conditions and that, as shown for RibBAs from other bacteria, the GTP cyclohydrolase II domain has no enzymatic activity. For this reason, we have renamed the annotated ribBA as ribBX. Because we were unable to identify other ribBA or ribA and ribB homologs in the genome of Bradyrhizobium ORS285, we hypothesize that the ORS285 strain can use unconventional enzymes or an alternative pathway for the initial steps of riboflavin biosynthesis. Inactivating ribBX has a drastic impact on the interaction of Bradyrhizobium ORS285 with many of the tested Aeschynomene spp. In these Aeschynomene spp., the ORS285 ribBX mutant is able to infect the plant host cells but the intracellular infection is not maintained and the nodules senesce early. This phenotype can be complemented by reintroduction of the 3,4-DHBP synthase domain alone. Our results indicate that, in Bradyrhizobium ORS285, the RibBX protein is not essential for riboflavin biosynthesis under free-living conditions and we hypothesize that its activity is needed to sustain riboflavin biosynthesis under certain symbiotic conditions. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Published: 2021

18. Promoting crop pest control by plant diversification in agricultural landscapes: A conceptual framework for analysing feedback loops between agro-ecological and socio-economic effects

Author: Aude Vialatte, Anaïs Tibi, Audrey Alignier, Valérie Angeon, Laurent Bedoussac, David A. Bohan, Douadia Bougherara, Alain Carpentier, Bastien Castagneyrol, Stéphane Cordeau, Pierre Courtois, Jean-Philippe Deguine, Jérôme Enjalbert, Frédéric Fabre, Fabienne Féménia, Hélène Fréville, Frédéric Goulet, Régis Grateau, Benoît Grimonprez, Nicolas Gross, Mourad Hannachi, Philippe Jeanneret, Laure Kuhfuss, Pierre Labarthe, Marie Launay, Marianne Lefebvre, Virginie Lelièvre, Stéphane Lemarié, Gilles Martel, Abel Masson, Mireille Navarrete, Manuel Plantegenest, Virginie Ravigné, Adrien Rusch, Frédéric Suffert, Abdoulaye Tapsoba, Olivier Therond, Sophie Thoyer, Vincent Martinet, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction de l'Expertise scientifique collective, de la Prospective et des Etudes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), Agroécologie [Dijon], 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Economie de l'Environnement - Montpellier - UMR 5211 (CEE-M), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Structures et Marché Agricoles, Ressources et Territoires (SMART-LERECO), AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Département Environnements et Sociétés (Cirad-ES), Economie Publique (ECO-PUB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Etudes et de Coopération Juridique Interdisciplinaire (CECOJI), Université de Poitiers, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Agroscope, University of St Andrews [Scotland], Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Groupe de Recherche Angevin en Economie et Management (GRANEM), Institut National de l'Horticulture et du Paysage-AGROCAMPUS OUEST-Université d'Angers (UA), Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), Laboratoire d'Economie Appliquée de Grenoble (GAEL), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), AGROCAMPUS OUEST-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), 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), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Agronomie et Environnement - Antenne Colmar (LAE-Colmar ), Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Economie de l'Environnement - Montpellier (CEE-M), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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)-INSTITUT AGRO Agrocampus Ouest, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Centre d’études et de coopération juridique interdisciplinaire - Université de Poitiers (CECOJI-UP), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de l'Horticulture et du Paysage, Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, French Office for Biodiversity (OFB) through the national ECOPHYTO plan, David A. Bohan, Alex J. Dumbrell, Adam J. Vanbergen, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), AGROCAMPUS OUEST, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de l'Horticulture et du Paysage-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 d'Angers (UA), 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)-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Gestion des ressources renouvelables et environnement (UPR GREEN), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Angers (UA)-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 l'Horticulture et du Paysage
Subjects: 2. Zero hunger, 0106 biological sciences, 13. Climate action, 11. Sustainability, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, 04 agricultural and veterinary sciences, 15. Life on land, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, 01 natural sciences, 010606 plant biology & botany, [SHS]Humanities and Social Sciences
Abstract: International audience; Given the negative environmental effects of conventional agricultural techniques, the need for biodiversity-friendly agriculture systems that rely more on ecosystem services and less on chemical inputs is becoming increasingly urgent. In this paper, we focus on crop protection strategies that are alternatives to the use of pesticides. Diversification of the plant component of agricultural areas at different space and time scales has been presented as a powerful socio-economic and agro-ecological mechanism for the sustainable control of pests. Our interdisciplinary group of scientific experts examined the literature on the ecological effects of plant diversification on pests and their natural enemies, as well as the social science literature on the conditions for farmers to adopt the corresponding practices, to assess the potential offered by plant diversification.We developed a conceptual framework that connects the agro-ecological and socio-economic components of an agricultural landscape in a dynamic loop accounting for interactions among elements at different spatial and temporal scales and their feedback effects. This article presents this framework and illustrates its application to the case of wheat production and protection. By explicitly connecting each level of agro-ecological organization with the potential socio-economic drivers and limitations underpinning the adoption and implementation of plant diversification in landscapes, this framework makes it possible to ana yse the synergies and antagonisms between different modes of diversification and the conditions of their deployment. Exploring this framework is a prerequisite to the identification of opportunities and key feed-back loops for designing diversification strategies that unlock the agro-ecological potential of f uture production systems. We conclude that there is a need for interdisciplinary research in experimental landscapes involving farmers and other local stakeholders to design sustainable future agricultural landscapes that deliver high levels of biological control services..
Published: 2022

19. One Health concepts and challenges for surveillance, forecasting and mitigation of plant disease beyond the traditional scope of crop production

Author: Nicolas Sauvion, Claire Nédellec, Ghislain Géniaux, Cindy E. Morris, Samuel Soubeyrand, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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 Montpellier (UM), Biostatistique et Processus Spatiaux (BioSP), ANR-17-CE32-0004,SPREE,Stratégie préemptive de surveillance de l'air et de l'eau pour anticiper l'émergence de maladies des plantes liés aux changements paysagers(2017), ANR-20-PCPA-0002,BEYOND,Building epidemiological surveillance and prophylaxis with observations both near and distant(2020), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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, agroecology, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, long distance dissemination, spillover, virulence drivers, Context (language use), Plant Science, Disease, Horticulture, Biology, 01 natural sciences, 03 medical and health sciences, disease forecasting, Genetics, Environmental planning, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Disease surveillance, Scope (project management), Health management system, 15. Life on land, Plant disease, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, One Health, 13. Climate action, Sustainable management, knowledge inference, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; The One Health approach to understanding disease epidemiology and achieving surveillance and prevention is holistic all while focusing on zoonotic diseases. Many of its principles are similar to those espoused in Agroecology, begetting the question of what One Health can contribute - in practice - to preventing plant disease. Here we describe four knowledge challenges for plant health management that have arisen from the One Health experience for zoonotic diseases that could boost prospects for novel approaches to plant disease surveillance, prediction and prevention. The challenges are to i) uncover reservoirs and revise pathogen life histories, ii) elucidate drivers of virulence beyond the context of direct host-pathogen interactions, iii) account for the natural highways of long distance dissemination (i.e., surface water and air mass movement), and iv) update disease forecasts in the face of changing land use, cultivation practices and climate. Furthermore, we note that implementation of a One Health approach to disease surveillance and prevention will require mobilization of tools to deal with the representation and accessibility of massive and heterogeneous data and knowledge; with knowledge inference, data science, modelling, and pattern recognition; and multi-actor approaches that unite different sectors of society as well as different scientific disciplines. The infrastructure to build and the obstacles to overcome for a bona fide One Health approach to disease surveillance and prevention are the key commonalities where actors in the efforts to prevent zoonotic diseases and plant disease can work together for human, animal and plant health and sustainable management of biodiversity.
Published: 2022

20. First report of rice brown spot caused by Exserohilum rostratum in Mali

Author: Kaboré, Kouka Hilaire, Diagne, Diariatou, Milazzo, Joelle, Adreit, Henri, Lebrun, Marc-Henri, Tharreau, Didier, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), University of Bamako [Mali], Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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 Montpellier (UM), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RICE CRP (grant to CIRAD), the Centre de Coopération Internationale en Recherche Agronomique pour le Développement, and The Islamic Bank of Development
Subjects: Subject Areas, Field crops, cereals and grains, [SDV]Life Sciences [q-bio], Fungi, food and beverages, Pathogen detection, Pathologie végétale, Maladie fongique, Causal Agent, Champignon pathogène, Maladie des plantes, [SDE]Environmental Sciences, Crop Type, H20 - Maladies des plantes
Abstract: International audience; Rice brown spot is an emerging disease of concern in many rice-growing countries. Different fungal species of the genera Bipolaris and Exserohilum were reported as the causal agents of this disease. These fungal pathogens cause similar necrotic lesions on leaves and infect grains with a significant effect on seed germination. In 2018, samples of rice seed and leaves with typical brown spot symptoms were collected from irrigated (Manikoura and Niono) and lowlands (M’pegnesso and Loulouni) rice fields in Mali and incubated for 5 to 7 days on wet filter paper at 25°C with 12 h photoperiod. Conidia observed under microscope were straight or slightly curved and light-brown or dark. They were also rostrate or obclavate and measured 31.4 to 275.6 x 7.3 to 18 µm (n=40). These morphological characteristics are identical to those of Exserohilum rostratum (Hernández-Restrepo et al. 2018). DNA from eight single-spored isolates was extracted by a CTAB-based protocol (Doyle and Doyle, 1987). Internal transcribed spacer (ITS) rDNA region, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and translation elongation factor 1 alpha (TEF1-α) genes were amplified by PCR with the primers ITS5/ITS4 (White et al. 1990), GPD1/GPD2 (Berbee et al. 1999) and EF1 983/EF1 2218 (Rehner et al. 2005), respectively. The amplicons were sequenced and deposited in NCBI GenBank. Sequence similarity between Malian strain was 100% for ITS and GAPDH, and 99.8-100% for TEF1. Sequence similarity between Malian strains and reference E. rostratum sequences BRIP 11417 (GenBank acc. no. LT837836, LT882553 and LT896656) and CBS 128061 (GenBank acc. no. KT265240, LT715900 and LT896658) were 99.6-100%. The maximum-likelihood phylogenetic tree generated with ITS, GAPDH and TEF1-α concatenated sequences, using MEGA-X 10.1.7 grouped all eight strains from Mali in the E. rostratum clade with a bootstrap value of 100%. For pathogenicity test, four strains from leaves and seed were grown on rabbit food agar (50 g/liter steeped filtrate of rabbit food pellets, Kaytee Products, Inc. Chilton, WI, USA, and 15 g agar) for 14 days at 25°C with a 12 h photoperiod (Hau and Rush 1980). Spores were collected and the concentration of spore suspension adjusted to 1.5 x 105 conidia/ml with 0.5% gelatin. The rice varieties ADNY 11, ARICA 9 and Shwetasoké were grown in pots with peat soil and NPK 13-5-18 at 3.5 g/liter of soil for 21 days. Four pots of each variety (5 seedlings/pot) were placed in a tray (60 plants per tray) and the leaves were sprayed with 30 ml of the conidial suspension or water at 0.5% gelatin (negative control). Plants were kept at maximum humidity (100%) at 21°C for one night and then transferred to a phytotron at 27°C. Seven days after inoculation, circular or oval foliar lesions of less than 5 mm long, either brown or dark, sometimes whitish in their centers were observed . These lesions were identical to those observed in the field. E. rostratum was reisolated from these lesions. E. rostratum affects a wide range of plant species, particularly grasses and has been observed on rice in many countries (Cardona and Gonzàlez 2007; Majeed et al. 2016; Silva et al. 2016; Toher et al. 2016). However, to our knowledge, this is the first report of E. rostratum causing brown spot in rice in Mali.
Published: 2022

21. Establishment of five new genera in the family Geminiviridae: Citlodavirus, Maldovirus, Mulcrilevirus, Opunvirus, and Topilevirus

Author: Jesús Navas-Castillo, Arvind Varsani, Darren P. Martin, F. Murilo Zerbini, Jean-Michel Lett, Elvira Fiallo-Olivé, Philippe Roumagnac, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto de Hortofruticultura Subtropical y Mediterranea 'La Mayora' (IHSM), Universidad de Málaga [Málaga] = University of Málaga [Málaga]-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidade Federal de Vicosa (UFV), Departemente de Fitopatologia/Bioagro, Universidade Federal de Viçosa (UFC), University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Arizona State University [Tempe] (ASU), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, European Union (ERDF), the Conseil Regional de La Reunion, and CIRAD., European Project: ERDF, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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 Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: food.ingredient, [SDV]Life Sciences [q-bio], Eragrovirus, Biology, Topocuvirus, 03 medical and health sciences, Mastrevirus, food, Virology, Turncurtovirus, Curtovirus, 030304 developmental biology, Plant Diseases, 0303 health sciences, 030306 microbiology, Begomovirus, Virion, General Medicine, Plants, biology.organism_classification, Geminiviridae, Metagenomics, Evolutionary biology, Becurtovirus
Abstract: International audience; Geminiviruses are plant-infecting, circular single-stranded DNA viruses that have a geminate virion morphology. These viruses infect both cultivated and non-cultivated monocotyledonous and dicotyledonous plants and have a wide geographical distribution. Nine genera had been established within the family Geminiviridae (Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastrevirus, Topocuvirus, and Turncurtovirus) as of 2020. In the last decade, metagenomics approaches have facilitated the discovery and identification of many novel viruses, among them numerous highly divergent geminiviruses. Here, we report the establishment of five new genera in the family Geminiviridae (Citlodavirus, Maldovirus, Mulcrilevirus, Opunvirus, and Topilevirus) to formally classify twelve new, divergent geminiviruses.
Published: 2022

22. Two distinctive Rhizobium genospecies nodulating Vicia villosa Roth in alkaline soils of Northwest China

Author: En Tao Wang, Shanshan Peng, Chunzeng Liu, Chen Guo, Junjie Zhang, Wenfeng Chen, Brigitte Brunel, Hou Pei, Shuo Li, Benyin Li, Yimin Shang, Zhengzhou University of Light Industry, Collaborative Innovation Center for Food Production and Safety of Henan Province, Partenaires INRAE, Henan Academy of Agricultural Sciences, Instituto Politecnico Nacional [Mexico] (IPN), State Key Laboratory of Agrobiotechnology, Research and Innovation Center of Chunlun Group, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), National Natural Science Foundation of China (NSFC) (31970006, 31400008), and Foundation of China Agriculture Research System - Green Manure CARS-22
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Genospecies, Soil Science, Plant Science, Northwest China, 01 natural sciences, Genetic diversity, Rhizobia, Soil pH, Rhizobium sophorae, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, 2. Zero hunger, biology, Phylogenetic tree, Villosa, food and beverages, 04 agricultural and veterinary sciences, Vicia villosa Roth, 15. Life on land, biology.organism_classification, 16S ribosomal RNA, Vicia villosa, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Rhizobium, 010606 plant biology & botany
Abstract: International audience; Aims To estimate the relative abundance, diversity and distribution of rhizobia associated with Vicia villosa Roth in soils of Northwest China. Method Rhizobia were trapped with V. villosa Roth plants from soils at seven sites and identified into genotypes by PCR-RFLP of IGS genes. They were further characterized by phylogenetic analyses of 16S rRNA, housekeeping genes (atpD, recA, glnII) and symbiotic genes (nodC). Soil physicochemical characteristics were recorded and Canonical Correlation Analysis was performed to correlate soil features and the distribution of IGS genotypes. Results 253 rhizobial strains were obtained from soils with pH 7.1-7.9. They were discriminated into 27 IGS types and further affiliated by phylogenetic analyses of 16S rRNA and multilocus sequence analysis (MLSA) into two clusters in Rhizobium. One corresponds to Rhizobium sophorae covering 228 strains in 25 IGS types and the other includes a novel genospecies containing two IGS types only detected in Shanxi Province, with higher soil pH and intermediate available phosphate and potassium contents. Representative strains of the novel genospecies show a specific phylogenetic nodC lineage, which may reflect differences in symbiosis properties. Furthermore, the Shanxi site was the less IGS diversified, based on Shannon diversity indices varying from 0.96 to 2.19 along the sampled area. Conclusions As the first study on diversity of rhizobia nodulating V. villosa Roth in China, R. sophorae and a novel Rhizobium genospecies with specific symbiotic genes were identified; and biogeographic patterns were found, mainly directed by soil pH, organic matter and soil salinity, including available phosphorus salts.
Published: 2020

23. Plant Viruses Can Alter Aphid-Triggered Calcium Elevations in Infected Leaves

Author: Then, Christiane, Bellegarde, Fanny, Schivre, Geoffrey, Martinière, Alexandre, Macia, Jean-Luc, Xiong, Tou, Drucker, Martin, Xiong, Tou Cheu, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Nagoya University
Subjects: 0106 biological sciences, calcium signalling, Arabidopsis thaliana, QH301-705.5, [SDV]Life Sciences [q-bio], Arabidopsis, aphid feeding activity, 01 natural sciences, Article, Plant Viruses, 03 medical and health sciences, Caulimovirus, Animals, turnip mosaic virus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Calcium Signaling, Biology (General), 030304 developmental biology, 0303 health sciences, defences, cauliflower mosaic virus, turnip yellows virus, green peach aphid, transmission, Arabidopsis Proteins, fungi, food and beverages, General Medicine, Plant Leaves, Aphids, Mutation, Calcium, 010606 plant biology & botany
Abstract: International audience; Alighting aphids probe a new host plant by intracellular test punctures for suitability. These induce immediate calcium signals that emanate from the punctured sites and might be the first step in plant recognition of aphid feeding and the subsequent elicitation of plant defence responses. Calcium is also involved in the transmission of non-persistent plant viruses that are acquired by aphids during test punctures. Therefore, we wanted to determine whether viral infection alters calcium signalling. For this, calcium signals triggered by aphids were imaged on transgenic Arabidopsis plants expressing the cytosolic FRET-based calcium reporter YC3.6-NES and infected with the non-persistent viruses cauliflower mosaic (CaMV) and turnip mosaic (TuMV), or the persistent virus, turnip yellows (TuYV). Aphids were placed on infected leaves and calcium elevations were recorded by time-lapse fluorescence microscopy. Calcium signal velocities were significantly slower in plants infected with CaMV or TuMV and signal areas were smaller in CaMV-infected plants. Transmission tests using CaMV-infected Arabidopsis mutants impaired in pathogen perception or in the generation of calcium signals revealed no differences in transmission efficiency. A transcriptomic meta-analysis indicated significant changes in expression of receptor-like kinases in the BAK1 pathway as well as of calcium channels in CaMV- and TuMV-infected plants. Taken together, infection with CaMV and TuMV, but not with TuYV, impacts aphid-induced calcium signalling. This suggests that viruses can modify plant responses to aphids from the very first vector/host contact.
Published: 2021
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24. A novel robust and high‐throughput method to measure cell death in Nicotiana benthamiana leaves by fluorescence imaging

Author: Xi, Yuxuan, Chochois, Vincent, Kroj, Thomas, Cesari, Stella, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Démarche intégrée pour l'obtention d'aliments de qualité (UMR QualiSud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut Agro - Montpellier SupAgro, Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), European Research Council (ERC-2019-STG-852482-ii-MAX), China Scholarship Council (CSC PhD grant 201806350131), ANR-18-CE20-0016,MagMAX,Structure, évolution et fonction d'effecteurs de virulence fongiques(2018), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Plant Leaves, cell death, Technical Advance, fluorescence imaging, quantitative analysis, Optical Imaging, Tobacco, fungi, Nicotiana benthamiana, food and beverages, Agrobacterium, immune response, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: Assessing immune responses and cell death in Nicotiana benthamiana leaf agro‐infiltration assays is a powerful and widely used experimental approach in molecular plant pathology. Here, we describe a reliable high‐throughput protocol to quantify strong, macroscopically visible cell death responses in N. benthamiana agro‐infiltration assays. The method relies on measuring the reduction of leaf autofluorescence in the red spectrum upon cell death induction and provides quantitative data suitable for straightforward statistical analysis. Two different well‐established model nucleotide‐binding and leucine‐rich repeat domain proteins (NLRs) were used to ensure the genericity of the approach. Its accuracy and versatility were compared to visual scoring of the cell death response and standard methods commonly used to characterize NLR activities in N. benthamiana. A discussion of the advantages and limitations of our method compared to other protocols demonstrates its robustness and versatility and provides an effective means to select the best‐suited protocol for a defined experiment., We provide a high‐throughput method to quantify cell death in Nicotiana benthamiana agro‐infiltration assays relying on the measurement of leaf red fluorescence decline upon induction of cell death.
Published: 2021

25. High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans

Author: Frank Nitsche, Karoline Hermanns, Alexandra Schoenle, Frédéric Mahé, Hartmut Arndt, Colomban de Vargas, Manon Hohlfeld, University of Cologne, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ECOlogy of MArine Plankton (ECOMAP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR)
Subjects: 0106 biological sciences, 0301 basic medicine, Geologic Sediments, QH301-705.5, [SDV]Life Sciences [q-bio], Euglenozoa, Biodiversity, Medicine (miscellaneous), Foraminifera, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Deep sea, Article, General Biochemistry, Genetics and Molecular Biology, Microbial ecology, 03 medical and health sciences, Algae, medicine, 14. Life underwater, Ciliophora, Kinetoplastida, Biology (General), Atlantic Ocean, Trophic level, Pacific Ocean, biology, Ecology, Protist, Pelagic zone, biology.organism_classification, Biooceanography, 030104 developmental biology, General Agricultural and Biological Sciences
Abstract: Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans., Alexandra Schoenle et al. use DNA metabarcoding and cultivation-based surveys of 11 regions in the Pacific and Atlantic Oceans encompassing the bathyal, abyssal, and hadal zones to identify the role of deep-sea heterotrophic protists relative to other trophic levels. Their results demonstrate that protistan species richness was locally specific and greater than that of metazoans and that measured in pelagic samples, and that deep-sea protist communities are relatively distinct from their pelagic counterparts.
Published: 2021

26. Rhizobia use a pathogenic-like effector to hijack leguminous nodulation signalling

Author: Hien P. Nguyen, Takakazu Kaneko, Safirah Tasa Nerves Ratu, Shin Okazaki, Albin Teulet, Eric Giraud, Michiko Yasuda, Makoto Hayashi, Shusei Sato, Sachiko Masuda, Hiroki Miwa, Tokyo University of Agriculture and Technology (TUAT), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Kyoto Sangyo University, RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), ANR-16-CE20-0013,SymEffectors,Système de sécrétion de type 3 pour la symbiose fixatrice d'azote(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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, Xanthomonas, Science, [SDV]Life Sciences [q-bio], Mutant, medicine.disease_cause, Plant Root Nodulation, Plant Roots, 01 natural sciences, Article, Type three secretion system, Rhizobia, Transcriptome, 03 medical and health sciences, Symbiosis, Gene Expression Regulation, Plant, medicine, Bradyrhizobium, Rhizobial symbiosis, Multidisciplinary, biology, Effector, fungi, food and beverages, Fabaceae, Pathogenic bacteria, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Xanthomonas campestris, Cell biology, 030104 developmental biology, Medicine, Soybeans, Root Nodules, Plant, Rhizobium, Signal Transduction, 010606 plant biology & botany
Abstract: Legume plants form a root-nodule symbiosis with rhizobia. This symbiosis establishment generally relies on rhizobium-produced Nod factors (NFs) and their perception by leguminous receptors (NFRs) that trigger nodulation. However, certain rhizobia hijack leguminous nodulation signalling via their type III secretion system, which functions in pathogenic bacteria to deliver effector proteins into host cells. Here, we report that rhizobia use pathogenic-like effectors to hijack legume nodulation signalling. The rhizobial effector Bel2-5 resembles the XopD effector of the plant pathogen Xanthomonas campestris and could induce nitrogen-fixing nodules on soybean nfr mutant. The soybean root transcriptome revealed that Bel2-5 induces expression of cytokinin-related genes, which are important for nodule organogenesis and represses ethylene- and defense-related genes that are deleterious to nodulation. Remarkably, Bel2-5 introduction into a strain unable to nodulate soybean mutant affected in NF perception conferred nodulation ability. Our findings show that rhizobia employ and have customized pathogenic effectors to promote leguminous nodulation signalling.
Published: 2021

27. An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection

Author: Reshetnyak, Ganna, Jacobs, Jonathan M., Auguy, Florence, Sciallano, Coline, Claude, Lisa, Medina, Clemence, Pérez-Quintero, Alvaro L., Comte, Aurore, Thomas, Emilie, Bogdanove, Adam J., Koebnik, Ralf, Szurek, Boris, Diévart, Anne, Brugidou, Christophe, Lacombe, Séverine, Cunnac, Sébastien, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Ohio State University [Columbus] (OSU), School of Integrative Plant Science [CALS], College of Agriculture and Life Sciences [Cornell University] (CALS), Cornell University [New York]-Cornell University [New York], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Ministère de l'Enseignement Supérieur et de la Recherche, Erasmus Mundus Action 2 PANACEA, PRECIOSA program of the European Community, National Science Foundation (NSF)DBI-1306196, ANR-14-CE19-0009,PIXIES,Extinction de l'immunité par des petits ARN végétaux induits par un pathogène bactérien(2014), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Cornell University [New York], and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Xanthomonas, Plant molecular biology, Science, [SDV]Life Sciences [q-bio], Small RNAs, food and beverages, Oryza, Article, Up-Regulation, Plant Leaves, Plant immunity, Gene Expression Regulation, Plant, RNA, Plant, RNA, Small Untranslated, Medicine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plant Diseases
Abstract: International audience; Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant–microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice ( Oryza sativa ) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas -induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20–22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system , a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis- genes have documented functions in immune signaling and xisRNA loci predominantly coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis -genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant–microbe interactions.
Published: 2021

28. Complex adaptive architecture underlies adaptation to quantitative host resistance in a fungal plant pathogen

Author: Véronique Roussel, Catherine Abadie, Sébastien Ravel, Luis Perez-Vicente, Jaime Aguayo, Jean Carlier, Thomas Dumartinet, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Instituto de Investigaciones de Sanidad Vegetal (INISAV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), European Agricultural Fund for Rural Development, Grant/Award Number: 31409-Cabaré, Agropolis Fondation Grant/Award Number: 1504-004-ESpace, European Regional Development Fund, CIRAD/ANSES, Conseil Regional de Guadeloupe, and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: 0106 biological sciences, Candidate gene, quantitative genetics, Acclimatization, Population, Genome Scan, genome scan, Quantitative trait locus, Biology, 010603 evolutionary biology, 01 natural sciences, MusaPseudocercospora fijiensis, 03 medical and health sciences, Genetics, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Plant Diseases, 2. Zero hunger, 0303 health sciences, education.field_of_study, Host (biology), Musa, Quantitative genetics, 15. Life on land, host adaptation, Adaptation, Physiological, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Plant Leaves, Host adaptation, Adaptation, fungal plant pathogen
Abstract: International audience; Plant pathogens often adapt to plant genetic resistance so characterization of the architecture underlying such an adaptation is required to understand the adaptive potential of pathogen populations. Erosion of banana quantitative resistance to a major leaf disease caused by polygenic adaptation of the causal agent, the fungus Pseudocercospora fijiensis, was recently identified in the northern Caribbean region. Genome scan and quantitative genetics approaches were combined to investigate the adaptive architecture underlying this adaptation. Thirty-two genomic regions showing host selection footprints were identified by pool sequencing of isolates collected from seven plantation pairs of two cultivars with different levels of quantitative resistance. Individual sequencing and phenotyping of isolates from one pair revealed significant and variable levels of correlation between haplotypes in 17 of these regions with a quantitative trait of pathogenicity (the diseased leaf area). The multilocus pattern of haplotypes detected in the 17 regions was found to be highly variable across all the population pairs studied. These results suggest complex adaptive architecture underlying plant pathogen adaptation to quantitative resistance with a polygenic basis, redundancy, and a low level of parallel evolution between pathogen populations. Candidate genes involved in quantitative pathogenicity and host adaptation of P. fijiensis were identified in genomic regions by combining annotation analysis with available biological data.
Published: 2021

29. Potential alien ranges of European plants will shrink in the future, but less so for already naturalized than for not yet naturalized species

Author: Carsten Hobohm, Florian Jansen, Petr Pyšek, Idoia Biurrun, Trevor S. Fristoe, Mark van Kleunen, Milan Chytrý, Robin Pouteau, Carsten Meyer, Thomas Wohlgemuth, Wilfried Thuiller, Rense Haveman, Jan Pergl, Jens-Christian Svenning, Caroline Brunel, Franz Essl, Qiang Yang, Wayne Dawson, Jesper Erenskjold Moeslund, Bernd Lenzner, Jonathan Lenoir, Patrick Weigelt, Holger Kreft, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Taizhou University, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Masaryk University [Brno] (MUNI), Durham University, University of Vienna [Vienna], University of Konstanz, Europa-Universität Flensburg, University of Rostock, Georg-August-University = Georg-August-Universität Göttingen, Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), German Centre for Integrative Biodiversity Research (iDiv), Leipzig University, Aarhus University [Aarhus], Charles University [Prague] (CU), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, University of the Basque Country [Bizkaia] (UPV/EHU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Duke University [Durham], University of Göttingen - Georg-August-Universität Göttingen, and Centre National de la Recherche Scientifique (CNRS)-Université de Picardie Jules Verne (UPJV)
Subjects: 0106 biological sciences, Vascular plant, land use change, 010504 meteorology & atmospheric sciences, distributional range shift, Range (biology), shifts, [SDE.MCG]Environmental Sciences/Global Changes, Species distribution, Biome, biological invasions, Climate change, Alien, migration, 010603 evolutionary biology, 01 natural sciences, flora, ecological-niche, topography, invasions, vegetation, ddc:570, alien plant species, interacting effect of global changes, Ecology, Evolution, Behavior and Systematics, Macroecology, 0105 earth and related environmental sciences, 2. Zero hunger, CLIMATE-CHANGE, biology, Ecology, species distribution model, Alien plant species, biological invasions, climate change, distributional range shift, interacting effect of global changes, land use change, macroecology, migration, non-analogue climate, species distribution model, prediction, 15. Life on land, biology.organism_classification, distribution models, uncertainties, Defensie, non-analogue climate, Geography, climate change, 13. Climate action, Alien plant species, macroecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Global biodiversity
Abstract: Aims The rapid increase in the number of species that have naturalized beyond their native range is among the most apparent features of the Anthropocene. How alien species will respond to other processes of future global changes is an emerging concern and remains poorly misunderstood. We therefore ask whether naturalized species will respond to climate and land use change differently than those species not yet naturalized anywhere in the world. Location Global. Methods We investigated future changes in the potential alien range of vascular plant species endemic to Europe that are either naturalized (n = 272) or not yet naturalized (1,213) outside of Europe. Potential ranges were estimated based on projections of species distribution models using 20 future climate-change scenarios. We mapped current and future global centres of naturalization risk. We also analysed expected changes in latitudinal, elevational and areal extent of species' potential alien ranges. Results We showed a large potential for more worldwide naturalizations of European plants currently and in the future. The centres of naturalization risk for naturalized and non-naturalized plants largely overlapped, and their location did not change much under projected future climates. Nevertheless, naturalized plants had their potential range shifting poleward over larger distances, whereas the non-naturalized ones had their potential elevational ranges shifting further upslope under the most severe climate change scenarios. As a result, climate and land use changes are predicted to shrink the potential alien range of European plants, but less so for already naturalized than for non-naturalized species. Main conclusions While currently non-naturalized plants originate frequently from mountain ranges or boreal and Mediterranean biomes in Europe, the naturalized ones usually occur at low elevations, close to human centres of activities. As the latter are expected to increase worldwide, this could explain why the potential alien range of already naturalized plants will shrink less. We thank Marten Winter (iDiv, Germany) and all who contributed to the GloNAF and EVA databases without whom this work would not have been possible. Robin Pouteau was supported by the National Natural Science Foundation of China (grant number 31901176) and Taizhou University (2018YQ001). Idoia Biurrun was supported by the Basque Government (IT936-16). Milan Chytry was supported by the Czech Science Foundation (19-28491X). Franz Essl and Bernd Lenzner appreciate funding by the Austrian Science Foundation FWF (I2086-B16). Carsten Meyer acknowledges funding by the Volkswagen Foundation through a Freigeist Fellowship (A118199), and additional support by iDiv, funded by the German Research Foundation (DFG-FZT 118, 202548816). Petr Pysek and Jan Pergl were supported by EXPRO grant (19-28807X) of the Czech Science Foundation and long-term research development project RVO (67985939) of Czech Academy of Sciences. Jens-Christian Svenning considers this work a contribution to his VILLUM Investigator project "Biodiversity Dynamics in a Changing World" funded by VILLUM FONDEN (16549). We appreciate the helpful comments by three anonymous reviewers and the Handling Editor, Raimundo Real.
Published: 2021

30. Metagenomic analysis of nepoviruses: diversity, evolution and identification of a genome region in members of subgroup A that appears to be important for host range

Author: Marc Fuchs, A S Spilmont, J Kubina, Jean-Sébastien Reynard, Jean-Michel Hily, Nils Poulicard, Olivier Lemaire, Emmanuelle Vigne, Institut Français de la Vigne et du Vin (IFV), Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Agroscope, Cornell University [New York], projects VACCIVINE and GPGV of the 'Plan National Deperissement du vignoble' (French Ministry of Agriculture, FranceAgrimer and CNIV), ANR-20-CE20-0010,URIVir,Rôles pro- and anti-viraux de l'uridylation des ARN chez les plantes(2020), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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, Nepovirus, Genome, Viral, 01 natural sciences, Genome, Host Specificity, Virus, Evolution, Molecular, Arabis mosaic virus, Open Reading Frames, 03 medical and health sciences, Virology, Plant virus, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Secoviridae, Phylogeny, 030304 developmental biology, Recombination, Genetic, Genetics, 0303 health sciences, biology, Genetic Variation, Grapevine fanleaf virus, General Medicine, Plants, biology.organism_classification, Phylogeography, Metagenomics, RNA, Viral, Original Article, 010606 plant biology & botany
Abstract: Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.
Published: 2021

31. Functional land cover scale for three insect pests with contrasting dispersal strategies in a fragmented coffee-based landscape in Central Kenya

Author: Abdelmutalab G.A. Azrag, John Odindi, Onisimo Mutanga, Tobias Landmann, Henri E. Z. Tonnang, Guillaume David, Elfatih M. Abdel-Rahman, Gladys Mosomtai, Régis Babin, International Centre of Insect Physiology and Ecology (ICIPE), ICIPE, University of KwaZulu-Natal (UKZN), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UK's Foreign, Commonwealth & Development Office (FCDO), the Swedish Interna-tional Development Cooperation Agency (Sida), the Swiss Agency for Development and Cooperation (SDC), the Federal Democratic Republic of Ethiopia, and and the Government of the Republic of Kenya. The views expressed herein do not necessarily reflect the official opinion of the donors. Gladys Mosomtai was supported by the In-Region Postgraduate Scholarship from the German Academic Exchange Service (DAAD) , Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD) and LOreal-UNESCO For Women in Science Fellowship.
Subjects: 0106 biological sciences, Coffea, medicine.disease_cause, 01 natural sciences, Abundance (ecology), 2. Zero hunger, Antestiopsis, Antestiopsis facetoides, Ravageur des plantes, Ecology, biology, Agroforestry, 04 agricultural and veterinary sciences, Écologie des populations, Geography, Antestiopsis thunbergii, Insecte nuisible, Plantations, Landscape ecology, Land cover, Landscape scale, 010603 evolutionary biology, Infestation, medicine, Hypothenemus hampei, fragmentation de l'habitat, business.industry, Pest control, Redundancy analysis, 15. Life on land, biology.organism_classification, H10 - Ravageurs des plantes, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Biological dispersal, Animal Science and Zoology, PEST analysis, Paysage agricole, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Agronomy and Crop Science
Abstract: International audience; In the Eastern Africa highlands, the gradual transformation of natural ecosystems to smallholding coffee-based agrosystems has resulted in more fragmented landscapes. Major pests of coffee find appropriate living conditions leading to high infestation rates and the need for smallholder farmers to implement pest control measures. This study aims to understand the influence of landscapes on the ecology of three major coffee pests: the coffee berry borer (CBB), Hypothenemus hampei, and the Antestia bugs Antestiopsis thunbergii (ABT) and A. facetoides (ABF). The study was conducted on a typical smallholder coffee-based landscape in central Kenya. The pest abundance was assessed monthly for two years in a network of 30 coffee plots spread across the coffee agro-ecological subzones (AEsZ), namely upper midland UM1 and UM2, and the transition zones between UM1 and UM2 and between UM2 and UM3, herein referred to as TZ1 and TZ2, respectively. Landscape metrics, viz. patch density, Euclidean nearest neighbour distance, proximity index, contagion index, interspersion and juxtaposition index were derived from a spatially explicit land cover map, based on 10 m Sentinel 2 data for nine buffer zones of radius ranging from 50 m to 1000 m around each sampled plot. Redundancy analysis (RDA) was used to establish the relationships between the observed pest abundances and landscape metrics, elevation, and AEsZ. Landscape indicators achieved the highest correlation with the pest abundances within a 300 m radius (Adjusted R2 > 0.5). Whereas beyond 300 m landscape scale, the predictor variables resulted in weak relationships (Adjusted R2 < 0.5) between the pests abundance and landscape metrics. We noted a strong influence of elevation and adjacency to cropland on Antestia bug populations. Specifically, ABF populations were negatively correlated with low elevation, whereas ABT’s were positively correlated with high elevation zone. On the other hand, CBB was strongly influenced by contiguous coffee patches, especially in UM1 and UM2. Therefore, we recommend reducing connectivity between coffee patches for the management of CBB, whereas further studies should be conducted to identify secondary hosts of Antestia bugs that should not be adjacent or within coffee stands.
Published: 2021

32. Secondary metabolite effects of different cocoa genotypes on feeding preference of the mirid Sahlbergella singularis Hagl

Author: R. Dibanda Feumba, I. Mama Ngah, C.F. Bilong Bilong, P. B. Nsoga Etam, Raymond Joseph Mahob, Hermine Claudine Mahot, D. M. Taliedje, F. Edoun Ebouel, Rachid Hanna, Régis Babin, C. B. Bakwo Bassogog, Université de Yaoundé I, Institut de Recherche Agricole pour le Développement [Yaoundé] (IRAD), University of Buéa, Institut de Recherches Médicales et d'Etudes des Plantes Médicinales (IMPM), International Institute of Tropical Agriculture (IITA-Cameroon), International Institute of Tropical Agriculture [Nigeria] (IITA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of California [Los Angeles] (UCLA), University of California, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and public investment funds of Cameroon
Subjects: 0106 biological sciences, F60 - Physiologie et biochimie végétale, %22">Major , Secondary metabolite, Biology, 01 natural sciences, Toxicology, Feeding behavior, Attractiveness/antixenosis, Genotype, Plant defense against herbivory, medicine, Sahlbergella singularis, Theobroma cacao, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Herbivore, Ecology, food and beverages, Plant secondary metabolites, H10 - Ravageurs des plantes, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 010602 entomology, Biochemical analyses, Tolerantresistant varieties, Insect Science, Insect-plant interactions, Résistance aux organismes nuisibles, PEST analysis, Sahlbergella, Agronomy and Crop Science, 010606 plant biology & botany, medicine.drug
Abstract: International audience; Sahlbergella singularis is a major insect pest of cocoa in Cameroon. Conventional insecticides remain the most widely used option for mirid control, which unfortunately have adverse effects on the environment and human health. Improved methods of controlling this species, both environmentally friendly and inexpensive to farmers, are requirements. Varietal control based on the selection of resistant and/or tolerant genotypes can be an interesting approach. Nonetheless, the role of secondary metabolites (SMs) in cocoa defense against mirids is poorly documented; yet, these compounds are reported to be key elements in plant defense against herbivores. For this purpose, SMs of twelve cocoa genotypes were identified and quantified, as well as their impact on food preference by mirids. Food preference was assessed through microtests measuring cocoa attractiveness and antixenosis toward mirids. The results showed that cocoa genotypes were differently accepted as food by mirids, with a significant preference for hybrid IMC60 x SNK605 and a non-preference for T60/887. The ten other cocoa genotypes showed intermediate results. Five SMs classes: alkaloids, flavonoids, polyphenols, saponins, and tannins were identified. Their rates varied between cocoa genotypes: polyphenols > alkaloids > flavonoids > tannins, and saponins. Cocoa genotypes with high total phenolic contents were significantly preferred by S. singularis (r(alpha) = 0.86, R-2 = 74.0%, P < 0.001), while those with low saponins contents were lowly accepted (r(alpha) = - 0.83, R-2 = 68.9%, P < 0.015), independently of the levels of other SMs. Given SMs high potential to affect mirid feeding behavior, analyzing cocoa SMs composition may help in early selection of resistant cocoa varieties against S. singularis.
Published: 2021

33. Draft Genome Sequence Resource for the Orange Rust Pathogen of Sugarcane Puccinia kuehnii

Author: Cardenas, Daniela, Cheema, Jitender, Oppelaar, Theodora, Hincapie, Martha, Sood, Sushma, Zheng, Qiaolin, Carrillo-Tarazona, Yisel, Huguet-Tapia, Jose, Saunders, Diane, Comstock, Jack, Rott, Philippe, Cano, Liliana, University of Florida [Gainesville] (UF), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), John Innes Centre [Norwich], USDA-ARS : Agricultural Research Service, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Florida Sugar Cane League (project 00107475, fund F000057, and fund 660684), and the National Institute of Food and Agriculture project FLA-IRC-005637
Subjects: sugarcane, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Puccinia, rust fungus, food and beverages, plant pathogen
Abstract: International audience; Puccinia kuehnii is an obligate biotrophic fungal pathogen that causes orange rust of sugarcane, which is prevalent in many countries around the globe. In the United States, orange rust was first detected in sugarcane in Florida in 2007 and poses a persistent and economically damaging threat to the sugarcane industry in this region. Here, we generated the first genome assemblies for two isolates of P. kuehnii (1040 and 2143) collected in Florida in 2017 from two sugarcane cultivars, CL85-1040 and CP89-2143, respectively. These two rust genome resources will be of immense value for future genomic studies, particularly further exploration of the predicted secretomes that may help define key pathogenicity determinants for this economically important pathogen.
Published: 2021

34. Identification and Molecular Characterization of a Novel Hordeivirus Associated With Yellow Mosaic Disease of Privet (Ligustrum vulgare) in Europe

Author: Paul Gugerli, François Maclot, Jean-Sébastien Reynard, Olivier Schumpp, Silvia Turco, Isabelle Kellenberger, Justine Brodard, Mikhail M. Pooggin, Agroscope, University of Basel (Unibas), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), FP7 People Marie-Curie Actions grant 608422, INRAE SPE department ViroMix grant, Swiss National Science Foundation grant IZCNZ0-174857, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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, Microbiology (medical), Ligustrum vulgare, Ligustrum, Hordeivirus, Biology, phylogeny, 01 natural sciences, Microbiology, Deep sequencing, 03 medical and health sciences, distribution, genome, Gene, Original Research, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Mosaic virus, Privet, transmission, RNA, biology.organism_classification, QR1-502, siRNAs, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, RNA silencing, virions, 010606 plant biology & botany
Abstract: Wild plants serve as a large reservoir of known and yet-unknown viruses and as a source of viral pathogens of cultivated plants. Yellow mosaic disease of forest shrub Ligustrum vulgare (privet) was recurrently observed in Europe for more than 100 years. Using a universal virus identification approach based on deep sequencing and de novo assembly of viral small interfering (si)RNAs we identified a causative agent of this disease in Switzerland and reconstructed its complete 3-segmented RNA genome. Notably, a short 3′-terminal common region (CR) attached to each segment via a ∼53–71 nucleotide poly(A) tract, as determined by RT-PCR sequencing, was initially identified as an orphan siRNA contig with conserved tRNA-like secondary structure. Phylogenomic analysis classified this virus as a novel member in the genus Hordeivirus of family Virgaviridae, which we named ligustrum mosaic virus (LigMV). Similar to other hordeiviruses, LigMV formed rod-shape virions (visualized by electron microscopy), was transmitted through seeds and could also be mechanically transmitted to herbaceous hosts Chenopodium quinoa and Nicotiana benthamiana. Blot hybridization analysis identified genomic and subgenomic RNAs, sharing the 3′-CR and likely serving as monocistronic mRNAs for seven evolutionarily-conserved viral proteins including two subunits of viral RNA-dependent RNA polymerase, coat protein, triple gene block proteins mediating viral movement and cysteine-rich suppressor of RNA silencing. Analysis of size, polarity, and hotspot profiles of viral siRNAs suggested that they are produced by the plant antiviral Dicer-like (DCL) proteins DCL2 and DCL4 processing double-stranded intermediates of genomic RNA replication. Whole genome sequencing of French and Austrian isolates of LigMV revealed its genetic stability over a wide geographic range (>99% nucleotide identity to Swiss isolates and each other), suggesting its persistence and spread in Europe via seed dispersal.
Published: 2021

35. Taxonomy update for the family Alphasatellitidae: new subfamily, genera, and species

Author: Bruno Gronenborn, Jean-Michel Lett, Jesús Navas-Castillo, Darren P. Martin, F. Murilo Zerbini, John E. Thomas, Philippe Roumagnac, Elvira Fiallo-Olivé, John W. Randles, H. Josef Vetten, Arvind Varsani, School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, University of Cape Town, Structural Biology Research Unit [Cape Town], Department of Integrative Biomedical Sciences [Cape Town], University of Cape Town-University of Cape Town, Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, School of Agriculture, Food and Wine, University of Adelaide, adresse personnelle [Allemagne], Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Instituto de Hortofruticultura Subtropical y Mediterranea 'La Mayora' (IHSM), Universidad de Málaga [Málaga] = University of Málaga [Málaga]-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Universidade Federal de Vicosa (UFV), Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and JML is supported by the European Union (ERDF), the Conseil Regional de La Reunion, and CIRAD.
Subjects: 0303 health sciences, Subfamily, 030306 microbiology, DNA, Single-Stranded, General Medicine, Genome, Viral, Biology, biology.organism_classification, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Virology, 03 medical and health sciences, Geminiviridae, Genus, Evolutionary biology, Viruses, Nanoviridae, Humans, Taxonomy (biology), 030304 developmental biology
Abstract: International audience; Alphasatellites (family Alphasatellitidae) are circular, single-stranded DNA molecules (similar to 1-1.4 kb) that encode a replication-associated protein and have commonly been associated with some members of the families Geminiviridae, Nanoviridae, and Metaxyviridae (recently established). Here, we provide a taxonomy update for the family Alphasatellitidae following the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021. The taxonomic update includes the establishment of the new subfamily Petromoalphasatellitinae. This new subfamily includes three new genera as well as the genus Babusatellite, which previously belonged to the subfamily Nanoalphasatellitinae. Additionally, three new genera and 14 new species have been established in the subfamily Geminialphasatellitinae, as well as five new species in the subfamily Nanoalphasatellitinae.
Published: 2021

36. Combining Implications and Conceptual Analysis to Learn from a Pesticidal Plant Knowledge Base

Author: Lina Mahrach, Alain Gutierrez, Pierre Martin, Pierre Silvie, Pascal Marnotte, Marianne Huchard, Priscilla Keip, Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Models And Reuse Engineering, Languages (MAREL), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Braun T., Gehrke M., Hanika T., Hernandez N., ANR-16-CONV-0004,DIGITAG,Institut Convergences en Agriculture Numérique(2016), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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: Knowledge management, Computer science, Formal Concept Analysis, Implication Rules, 02 engineering and technology, Scientific literature, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, Formal concept analysis, One Health, 2. Zero hunger, business.industry, fungi, food and beverages, Relational concept analysis, 15. Life on land, Readability, Knowledge base, Life Sciences Knowledge Base, Organic farming, Duquenne-Guigues basis, 020201 artificial intelligence & image processing, Relational Concept Analysis, business, Meaning (linguistics)
Abstract: Post-Recording of the talk: https://video.umontpellier.fr/video/13887-iccs2021-lina-mahrach-talk/; International audience; Supporting organic farming aims to find alternative solutions to synthetic pesticides and antibiotics, using local plants, to protect crops. Moreover, in the One Health approach (OHA), a pesticidal plant should not be harmful to humans, meaning it cannot be toxic if the crop is consumed or should have a limited and conscious use if it is used for medical care. Knowledge on plant use presented in the scientific literature was compiled in a knowledge base (KB). The challenge is to develop a KB exploration method that informs experts (including farmers) about protection systems properties that respect OHA. In this paper, we present a method that extracts the Duquenne-Guigues basis of implications from knowledge structured using Relational Concept Analysis (RCA). We evaluate the impact of three data representations on the implications and their readability. The experimentation is conducted on 562 plant species used to protect 15 crops against 29 pest species of the Noctuidae family. Results show that consistently splitting data into several tables fosters less redundant and more focused implications.
Published: 2021

37. One Plant Health

Author: Thébaud, Gaël, Urbino, Cica, Dallot, Sylvie, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2021

38. Shade tree traits and microclimate modifications: Implications for pathogen management in biodiverse coffee agroforests

Author: Stephanie Gagliardi, Jacques Avelino, Elias de Melo Virginio Filho, Marney E. Isaac, University of Toronto [Scarborough, Canada], Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Centro Agronómico Tropical de Investigación y Enseñanza - Tropical Agricultural Research and Higher Education Center (CATIE), and Natural Sciences and Engineering Research Council of Canada
Subjects: 0106 biological sciences, Canopy, Costa Rica, Microclimate, Biodiversity, Biology, 01 natural sciences, agroforestry, diversity, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, leaf functional traits, Ecology, Evolution, Behavior and Systematics, Leaf wetness, 2. Zero hunger, Hemileia vastatrix, Shade tree, 04 agricultural and veterinary sciences, Coffea arabica, 15. Life on land, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Agronomy, 040103 agronomy & agriculture, shade tree architecture, 0401 agriculture, forestry, and fisheries, Monoculture, Pruning, 010606 plant biology & botany
Abstract: International audience; Diversified coffee agroforests modify microclimate conditions in comparison with monocultures, impacting the success of significant plant pathogens, such as Hemileia vastatrix, which causes coffee leaf rust (CLR). However, research is often limited to the dichotomous analysis of shaded agroforestry systems or unshaded monocultures, often overlooking the nuanced effect of shade tree trait diversity. Our study aims to determine the cumulative effects of shade tree canopy architectural characteristics and leaf functional traits in biodiverse agroforests on microclimate modifications and CLR incidence. We measured plot-level microclimate conditions (air temperature, relative humidity, leaf wetness duration, throughfall kinetic energy) in three single-stratum and two double-strata shade tree canopy treatments, including Erythrina poeppigiana, Terminalia amazonia, and Chloroleucon eurycyclum. Commonly reported canopy characteristics and leaf traits were compared to average microclimate conditions and CLR incidence levels. We found that shade tree trait expression significantly explained most microclimate conditions, and that two key shade tree traits (canopy openness, leaf area) significantly explain CLR incidence levels (R-2 = 0.211, p = 0.036). Our results highlight the differences in microclimate conditions and CLR incidence among biodiverse agroforests, as well as the important explanatory power of shade tree traits. Specific effects of shade tree traits on pathogen dynamics can directly inform agroforestry system design (i.e., shade tree species selection) and sustainable coffee farm management practices (i.e., pruning practices).
Published: 2021

39. Occurrence of two races of Puccinia kuehnii causing orange rust of sugarcane in Florida

Author: Santosh Sanjel, Richard N. Raid, Martha Hincapie, Yunwen Wang, James Todd, Sushma Sood, Bhim Chaulagain, Philippe Rott, Jack C. Comstock, University of Florida [Gainesville] (UF), USDA-ARS : Agricultural Research Service, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Florida Sugar Cane League, Grant/Award Number: 660684, F000057 and 00107475
Subjects: 0106 biological sciences, 0301 basic medicine, Pouvoir pathogène, Plant Science, Orange (colour), Horticulture, 01 natural sciences, Rust, Agent pathogène, Pucciniales, Saccharum, 03 medical and health sciences, Variation génétique, Genetic variation, Genetics, Cultivar, Variété, AFLPdetached leaf assaySaccharum spp, Puccinia kuehnii, H20 - Maladies des plantes, biology, Inoculation, food and beverages, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, Amplified fragment length polymorphism, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Orange rust of sugarcane caused by Puccinia kuehnii was first reported in Florida in 2007. Since then, several sugarcane cultivars that were resistant during the initial epidemics became susceptible within a few years. These shifts in resistance were attributed to the evolution of the pathogen and appearance of new races. To study the variation in virulence of P. kuehnii, healthy leaf pieces of sugarcane cultivars susceptible to orange rust were brush inoculated with isolates of P. kuehnii collected from susceptible cultivars in the field. After inoculation, leaf pieces were placed in an incubator and disease severity based on the number of rust uredinia was determined 2 weeks postinoculation. Isolates of P. kuehnii collected from sugarcane cultivar CP 89-2143, which only showed severe symptoms of orange rust starting in 2011-2012, produced 300%-500% more uredinia on CP 89-2143 than the isolates collected from cultivar CL 85-1040 that has been susceptible since 2007. Sugarcane cultivar CL 85-1040 exhibited high and equivalent numbers of uredinia regardless of the inoculated isolate of the pathogen. These data support the occurrence of pathogenic specialization within P. kuehnii and the existence of at least two races of this pathogen in Florida. Analysis of amplified fragment-length polymorphism among isolates of P. kuehnii from cultivars CP 89-2143 and CL 85-1040 differing in resistance to orange rust revealed genetic variation among rust uredinia. However, this variation was not associated with a specific sugarcane cultivar, suggesting that pathogenic variation was not linked to major, but rather to small genetic changes within the genome of P. kuehnii.
Published: 2021

40. Arachis hypogaea L. from Acid Soils of Nanyang (China) Is Frequently Associated with Bradyrhizobium guangdongense and Occasionally with Bradyrhizobium ottawaense or Three Bradyrhizobium Genospecies

Author: Shuo Li, Brigitte Brunel, Wenfeng Chen, Jiangchun Song, Euan K. James, Junjie Zhang, Mitchell Andrews, En Tao Wang, Shanshan Peng, Zhengzhou University of Light Industry, Collaborative Innovation Center for Food Production and Safety of Henan Province, Partenaires INRAE, Nan Yang Academy of Sciences, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Inst Politecn Nacl, CICATA, Queretaro 76090, Mexico, Instituto Politecnico Nacional [Mexico] (IPN), The James Hutton Institute, State Key Laboratory for Agrobiotechnology, China Agricultural University (CAU), University of Lincoln, and Project for Extramural Scientists of State Key Laboratory of Agrobiotechnology2021SKLAB6-8
Subjects: DNA, Bacterial, MLSA, Arachis, Genospecies, Soil Science, Rhizobia, Bradyrhizobium ottawaense, Bradyrhizobium, 03 medical and health sciences, Soil, Symbiosis, RNA, Ribosomal, 16S, Botany, IAA production, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Lespedeza cuneata, Ecology, biology, Phylogenetic tree, food and beverages, Soil classification, Fabaceae, 04 agricultural and veterinary sciences, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, 15. Life on land, biology.organism_classification, 16S ribosomal RNA, Peanut, [SDE]Environmental Sciences, 040103 agronomy & agriculture, bacteria, 0401 agriculture, forestry, and fisheries, Root Nodules, Plant, Rhizobium
Abstract: International audience; Henan Province is a major area of peanut production in China but the rhizobia nodulating the crop in this region have not been described. A collection of 217 strains of peanut rhizobia was obtained from six field sites across four soil types in Henan Province, North China, by using peanut as a trap host under glasshouse conditions. The 217 strains separated into 8 distinct types on PCR-RFLP analysis of their IGS sequences. Phylogenetic analysis of the 16S rRNA, recA, atpD, and glnII genes of 11 representative strains of the 8 IGS types identified Bradyrhizobium guangdongense, B. ottawaense and three novel Bradyrhizobium genospecies. Bradyrhizobium guangdongense was dominant, accounting for 75.0% of the total isolates across the field sites while B. ottawaense covered 5.1% and the three novel Bradyrhizobium genospecies 4.1 to 8.8% of the total. The symbiosis-related nodA and nifH gene sequences were not congruent with the core genes on phylogenetic analysis and separated into three groups, two of which were similar to sequences of Bradyrhizobium spp. isolated from peanut in south-east China and the third identical to that of B. yuanmingense isolated from Lespedeza cuneata in northern China. A canonical correlation analysis between the distribution of IGS genotypes and soil physicochemical characteristics and climatic factors indicated that the occurrence of IGS types/species was mainly associated with soil pH and available phosphorus.
Published: 2021

41. Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley

Author: Issaka, Souley, Traore, Oumar, Longue, Regis Dimitri Skope, Pinel-Galzi, Agnes, Gill, Mandev S, Dellicour, Simon, Bastide, Paul, Guindon, Stephane, Hebrard, Eugenie, Dugue, Marie-Jo, Sere, Yacouba, Semballa, Silla, Ake, Severin, Lemey, Philippe, Fargette, Denis, Université Boubakar Bâ de Tillabéri, Institut de l'Environnement et Recherches Agricoles [Ouagadougou] (INERA), Institut de Recherche pour le Développement (IRD), Université de Bangui, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Université libre de Bruxelles (ULB), Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Agronomy and Farming Systems, Institut du Développement Rural, Université Polytechnique Nazi Boni Bobo-Dioulasso (UNB), Université Félix Houphouët-Boigny (UFHB), ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), European Project: 0725422(2007), Centre national de la recherche scientifique et technologique [Ouagadougou] (CNRST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: AFRICA, [STAT.AP]Statistics [stat]/Applications [stat.AP], Science & Technology, fungi, landscape phylogeography, Généralités, Viral phylogeography, PERFORMANCE, molecular epidemiology, viral phylogeography, EMERGENCE, Virology, Molecular epidemiology, parasitic diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, disease ecology, EPIDEMIOLOGY, Disease ecology, Landscape phylogeography, Life Sciences & Biomedicine
Abstract: To investigate the spread of Rice yellow mottle virus (RYMV) along the Niger River, regular sampling of virus isolates was conducted along 500 km of the Niger Valley in the Republic of Niger and was complemented by additional sampling in neighbouring countries in West Africa and Central Africa. The spread of RYMV into and within the Republic of Niger was inferred as a continuous process using a Bayesian statistical framework applied previously to reconstruct its dispersal history in West Africa, East Africa, and Madagascar. The spatial resolution along this section of the Niger River was the highest implemented for RYMV and possibly for any plant virus. We benefited from the results of early field surveys of the disease for the validation of the phylogeographic reconstruction and from the well-documented history of rice cultivation changes along the Niger River for their interpretation. As a prerequisite, the temporal signal of the RYMV data sets was revisited in the light of recent methodological advances. The role of the hydrographic network of the Niger Basin in RYMV spread was examined, and the link between virus population dynamics and the extent of irrigated rice was assessed. RYMV was introduced along the Niger River in the Republic of Niger in the early 1980s from areas to the southwest of the country where rice was increasingly grown. Viral spread was triggered by a major irrigation scheme made of a set of rice perimeters along the river valley. The subsequent spatial and temporal host continuity and the inoculum build-up allowed for a rapid spread of RYMV along the Niger River, upstream and downstream, over hundreds of kilometres, and led to the development of severe epidemics. There was no evidence of long-distance dissemination of the virus through natural water. Floating rice in the main meanders of the Middle Niger did not contribute to virus dispersal from West Africa to Central Africa. RYMV along the Niger River is an insightful example of how agricultural intensification favours pathogen emergence and spread., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2021

42. Parameter Estimation in a PDE Model for the Spatial Spread of Cocoa Black Pod Disease

Author: Lionel Roques, Z. Ambang, P. Takam Soh, Samuel Soubeyrand, C. G. Nembot Fomba, G. M. ten Hoopen, Université de Yaoundé I, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biostatistique et Processus Spatiaux (BioSP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), DP Agroforesterie Cameroon, the French Government, and the French Embassy in Yaounde (SCAC)
Subjects: 0106 biological sciences, General Mathematics, Secondary infection, Immunology, Phytophthora megakarya, Model parameters, 01 natural sciences, Epidemiological modeling, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Pathosystem, Maladie des plantes, Shade, Statistics, Parameter estimation, Theobroma cacao, H20 - Maladies des plantes, 030304 developmental biology, General Environmental Science, Mathematics, 2. Zero hunger, Pharmacology, 0303 health sciences, biology, U10 - Informatique, mathématiques et statistiques, Estimation theory, General Neuroscience, fungi, food and beverages, Black pod rot, biology.organism_classification, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Épidémiologie, Point of delivery, Computational Theory and Mathematics, Modélisation, Shading, General Agricultural and Biological Sciences, Modèle mathématique, 010606 plant biology & botany
Abstract: International audience; In this paper, we develop an epidemiological model with both environmental (primary infection from the environmental spores reservoir) and direct transmission (secondary infection from an infected host to a susceptible pod). This model simulates the spatiotemporal evolution of cocoa black pod disease caused by Phytophthora megakarya. Since reliable parameter estimation is a central issue for modeling realistic biological systems, we used a mechanistic-statistical approach to estimate model parameters from real observations of a specific cocoa plot. In addition, to refine numerical simulations of the pathosystem, data describing the shade intensity all over the plot were exploited and led to increased model predictions accuracy and also highlighted a higher number of infected pods located in areas of the plot with higher shading intensity. Recommendations in terms of promoting cocoa farming in systems with low shading intensity may be evident if these results are confirmed. Our results also highlight the importance of the environmental spore reservoir in black pod disease dynamics.
Published: 2021

43. Stop helping pathogens: engineering plant susceptibility genes for durable resistance

Author: Garcia-Ruiz, Hernan, Szurek, Boris, Van den Ackerveken, Guido, Sub Plant-Microbe Interactions, Plant Microbe Interactions, Sub Plant-Microbe Interactions, Plant Microbe Interactions, University of Nebraska [Lincoln], University of Nebraska System, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Utrecht University [Utrecht], grant R01GM120108 and by the Nebraska Agricultural Experiment Station with funding from the Hatch Act (Accession Number 1007272) through the USDA National Institute of Food and Agriculture, grants of the Dutch Research Council (NWO), subawards to IRD from the Heinrich Heine University of Dusseldorf funded by the Bill & Melinda Gates Foundation, University of Nebraska–Lincoln, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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, Crops, Agricultural, Genetic resistance, Biomedical Engineering, Susceptibility gene, Bioengineering, Computational biology, Biology, 01 natural sciences, 03 medical and health sciences, Genome editing, 010608 biotechnology, Gene, 030304 developmental biology, Disease Resistance, Plant Diseases, 2. Zero hunger, Gene Editing, 0303 health sciences, Resistance (ecology), business.industry, fungi, food and beverages, 15. Life on land, Plants, Genetically Modified, Plant disease, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Plant Breeding, Agriculture, business, Genetic Engineering, Biotechnology
Abstract: International audience; Alternatives to protect crops against diseases are desperately needed to secure world food production and make agriculture more sustainable. Genetic resistance to pathogens utilized so far is mostly based on single dominant resistance genes that mediate specific recognition of invaders and that is often rapidly broken by pathogen variants. Perturbation of plant susceptibility (S) genes offers an alternative providing plants with recessive resistance that is proposed to be more durable. S genes enable the establishment of plant disease, and their inactivation provides opportunities for resistance breeding of crops. However, loss of S gene function can have pleiotropic effects. Developments in genome editing technology promise to provide powerful methods to precisely interfere with crop S gene functions and reduce tradeoffs.
Published: 2021

44. Predictive Modeling of Brown Rust of Sugarcane Based on Temperature and Relative Humidity in Florida

Author: Philippe Rott, Ian M. Small, Bhim Chaulagain, Richard N. Raid, James M. Shine, University of Florida [Gainesville] (UF), Sugar Cane Growers Cooperative of Florida, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Florida Sugar Cane League (http://florida sugarcaneleague.org/), project 00107475 (PR), fund F000057 (PR), and fund 660684 (PR)
Subjects: 0106 biological sciences, Veterinary medicine, Plant Science, Logistic regression, 01 natural sciences, Rust, Maladie des plantes, Puccinia melanocephala, 2. Zero hunger, 0303 health sciences, U10 - Informatique, mathématiques et statistiques, Temperature, food and beverages, Saccharum, Rouille, Florida, Mean squared prediction error, Biology, Conditions météorologiques, 03 medical and health sciences, Disease severity, Relative humidity, 030304 developmental biology, Plant Diseases, H20 - Maladies des plantes, Humidity, Maladie fongique, 15. Life on land, Stepwise regression, biology.organism_classification, Température, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, ecology and epidemiology, Modélisation, Weather data, mycology, Humidité, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Logistic regression models were developed from 5 years (2014 to 2018) of disease severity and weather data in an attempt to predict brown rust of sugarcane at the Everglades Research and Education Center in Belle Glade, Florida. Disease severity (percentage area of the top visible dewlap leaf covered by rust) was visually assessed in the field every 2 weeks for two varieties susceptible to brown rust. A total of 250 variables were derived from weather data for 10- to 40-day periods before each brown rust assessment day. A subset of these variables were then evaluated as potential predictors of severity of brown rust based on their individual correlation or their biological meaningfulness. Analyses of correlation and stepwise logistic regression allowed us to identify afternoon humid thermal ratio (AHTR), temperature-based duration variables, and their interaction terms as the most significant variables associated with brown rust epidemics of sugarcane in Florida. The nine best predictive models were identified based on model accuracy, sensitivity, specificity, and estimates of the prediction error. The prediction accuracy of these models ranged from 73 to 85%. Single-variable model BR2 (based on AHTR) classified 89% of the epidemic and 81% of the nonepidemic status of the disease. More than 83% of the epidemics and 81% of the nonepidemic status of sugarcane brown rust was correctly classified via multiple-variable models. These models can be used as components of a rust disease warning system to assist in the management of brown rust epidemics of sugarcane in south Florida.
Published: 2021

45. A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Author: Eve Lucas, Renato Goldenberg, Robyn S. Cowan, Oscar Alejandro Pérez Escobar, William J. Baker, Edward Biffin, Kyle W. Tomlinson, Yee Wen Low, Shirley A. Graham, Deise Josely Pereira Gonçalves, Andrew H. Thornhill, Yohan Pillon, Augusto Giaretta, Tristan Charles-Dominique, Artemis Anest, Olivier Maurin, Peter G. Wilson, Darin S. Penneys, Steven Dodsworth, Félix Forest, Sarah K. Morris, Fiorella Fernanda Mazine, Peter C. Hoch, Niroshini Epitawalage, Gustavo Hiroaki Shimizu, Ian M. Turner, Catherine McGinnie, Alexandre R. Zuntini, Sidonie Bellot, Lisa Pokorny, Vanessa Graziele Staggemeier, Berta Gallego, Grace E. Brewer, Thais N. C. Vasconcelos, Fabián A. Michelangeli, Royal Botanic Gardens, Kew, Institute of Deep-Sea Science and Engineering [Chinese Academy of Sciences] [Sanya] (IDSSE), Chinese Academy of Sciences [Beijing] (CAS), University of Chinese Academy of Sciences [Beijing] (UCAS), State Herbarium South Australia, Sorbonne Université (SU), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Royal Botanic Gardens [Kew], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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, Crypteroniaceae, Myrtaceae, [SDV]Life Sciences [q-bio], Plant Science, 010603 evolutionary biology, 01 natural sciences, Coalescent theory, Magnoliopsida, 03 medical and health sciences, Combretaceae, Phylogenomics, Myrtales, Vochysiaceae, Genetics, Clade, Penaeaceae, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Alzateaceae, Cell Nucleus, Lythraceae, 0303 health sciences, biology, Phylogenetic tree, phylogenomics, 15. Life on land, biology.organism_classification, Onagraceae, Order (biology), Evolutionary biology, Melastomataceae
Abstract: International audience; Premise To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. Methods We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). Results Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. Conclusions High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.
Published: 2021

46. Genetic structure of Xanthomonas oryzae pv. oryzae populations, Talome diversity and resistance assessment of elite rice varieties in Burkina Faso

Author: Diallo, Amadou, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Université Montpellier, Université Ouaga 1 Professeur Joseph Ki-Zerbo (Ouagadougou, Burkina Faso), Boris Szurek, Mahamadou Sawadogo, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 Université Joseph Ki-Zerbo (Ouagadougou, Burkina Faso)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Diversity, Diversité, Xanthomonas oryzae pv. oryzae, Resistance gene, Gène de résistance, Gène d'avirulence, Rice, Avirulence gene, Riz
Abstract: Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice vascular bacterial blight (RBB), an important rice disease that causes considerable yield losses in many rice-growing regions of Asia and Africa. The pathogenesis of Xoo is highly dependent on Transcriptional Activator-Like (TAL) effectors that act as true eukaryotic transcription factors by inducing the expression of host susceptibility genes favorable to bacterial growth and disease development.Varietal resistance is considered to be the most effective and economical method of controlling vascular bacterial disease. Previous work has provided insight into some of the genetic and phenotypic characteristics of Burkinabe Xoo strains. These strains are from a different genetic group than the Asian group and are characterized by a smaller number of genes encoding TAL effectors. Two races A1 and A2 of Xoo were characterized in Burkina Faso, indicating that the resistance genes Xa4, xa5 and Xa7 confer effective resistance to these two races. In addition, elite local rice varieties NERICA and FKR tested under artificial inoculation conditions were shown to be resistant to a broad spectrum of African Xoo strains. However, given the high degree of genetic variation in the pathogen, with pathotypes continually adapting to deployed resistance genes, there is a need both to know the diversity of effectors present and to have a continuous understanding of the genetic structure and evolutionary dynamics of pathogen populations in order to better manage the durability of resistance genes. Thus, the objectives of this thesis were (i) to analyze the genetic structure and evolutionary dynamics of Xoo pathogen populations collected in Burkina Faso between 2004 and 2018 based on microsatellite marker diversity, (ii) to evaluate the diversity and evolution of the TALome in these populations through races and the content of TAL effectors and (iii) to identify sources of effective resistance against BLB under semi-controlled conditions and to evaluate the resistance of elite varieties NERICA and FKR against Xoo populations in the fieldGenotyping of the collection using an MLVA scheme based on the study of 14 microsatellite loci developed previously allowed us to distinguish 22 haplotypes in Burkina Faso, including 18 for the Bagré site. Strains were discriminated according to collection sites for the years 2016 to 2018. The majority of the "old" strains are grouped within the same haplotype. Five haplotypes are shared by strains collected in two consecutive years: haplotype 3 includes strains collected in Bagré in 2017 and 2018 while the other four include strains collected in 2016 and 2017. We can also observe descent links at the Bagré site between 2016 and 2017. These results could indicate seed transmission of Xoo and the absence of new introductions. RFLP analysis of TAL effector diversity revealed eight different fingerprints for 177 strains analyzed. Interestingly, haplotypes 3, 7, 11 and 15 included several TALome fingerprints suggesting a recent evolution of TALomes. The strains collected recently in Burkina Faso belong to race A3, previously identified in Mali. These results improve our knowledge of the genetic structure of Xoo populations in Burkina Faso, an important prerequisite for guiding selection and deployment of resistance genes.; Xanthomonas oryzae pv. oryzae (Xoo) est l’agent causal de la bactériose vasculaire du riz (BLB), une importante maladie du riz qui cause des pertes de rendements considérables dans de nombreuses régions rizicoles en Asie et en Afrique. La pathogénie de Xoo est fortement dépendante des effecteurs de type TAL (Transcriptional Activator-Like) qui agissent comme de véritables facteurs de transcription eucaryotes en induisant l’expression de gènes de sensibilité de l’hôte favorables à la croissance bactérienne et au développement de la maladie.La résistance variétale est considérée comme la méthode de lutte la plus efficace et la plus économique contre la bactériose vasculaire. Des travaux antérieurs ont permis de comprendre certaines caractéristiques génétiques et phénotypiques des souches de Xoo burkinabè. Ces souches sont d’un groupe génétique différent du groupe asiatique et sont notamment caractérisées par un plus petit nombre de gènes codant les effecteurs TAL. Deux races A1 et A2 de Xoo ont été caractérisées au Burkina Faso, indiquant que les gènes de résistance Xa4, xa5 et Xa7 confèrent une résistance efficace à ces deux races. De plus, des variétés élites de riz local NERICA et FKR testées en conditions d’inoculation artificielles ont été montrées comme résistantes à un large spectre de souches de Xoo africaines. Toutefois, compte tenu du degré élevé de variation génétique de l’agent pathogène, avec des pathotypes qui s’adaptent continuellement aux gènes de résistance déployés, il est nécessaire à la fois de connaitre la diversité des effecteurs en présence et d’avoir une compréhension continuelle de la structure génétique et de la dynamique évolutive des populations pathogènes afin de mieux gérer la durabilité des gènes de résistance. Ainsi, les objectifs de cette thèse ont été (i) d’analyser la structure génétique et la dynamique évolutive des populations pathogènes de Xoo collectées au Burkina Faso entre 2004 et 2018 en s’appuyant sur la diversité de marqueurs de type microsatellites, (ii) d’évaluer la diversité et évolution du TALome dans ces populations à travers de races et le contenu en effecteurs de type TAL et (iii) d’identifier des sources de résistance efficaces contre la BLB en conditions semi contrôlées et évaluer la résistance des variétés élites NERICA et FKR contre les populations de Xoo au champ.Le génotypage de la collection à l’aide d’un schéma MLVA basé sur l’étude de 14 loci microsatellites développés précédemment a permis de distinguer 22 haplotypes au Burkina Faso dont 18 pour le site de Bagré. Les souches ont été discriminées selon les sites de collecte pour les années 2016 à 2018. La majorité des « anciennes » souches se retrouvent regroupées au sein d’un même haplotype. Cinq haplotypes sont partagés par des souches collectées sur deux années consécutives: l’haplotype 3 comporte des souches collectées à Bagré en 2017 et 2018 tandis que les 4 autres comportent des souches collectées en 2016 et 2017. On peut par ailleurs observer des liens de descendance au niveau du site de Bagré entre 2016 et 2017. Ces résultats pourraient témoigner d’une transmission de Xoo par les semences et de l’absence de nouvelles introductions. L’analyse de la diversité des effecteurs TAL par RFLP a révélé huit empreintes différentes pour 177 souches analysées. De façon intéressante, les haplotypes 3, 7, 11 et 15 comprennent plusieurs empreintes de TALomes ce qui suggère une évolution récente de ces derniers. Les souches collectées récemment au Burkina Faso, appartiennent à la race A3, auparavant identifiée au Mali. Ces résultats améliorent nos connaissances sur la structure génétique des populations de Xoo au Burkina Faso, un atout préalable important à l’orientation de la sélection et le déploiement des gènes de résistance.
Published: 2021

47. pr2-primers: an 18S rRNA primer database for protists

Author: David Bass, Frédéric Mahé, Daniel Vaulot, Stefan Geisen, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ECOlogy of MArine Plankton (ECOMAP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Nanyang Technological University [Singapour], Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Wageningen University and Research [Wageningen] (WUR), Nanjing Agricultural University, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), The Natural History Museum [London] (NHM), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Nanjing Agricultural University (NAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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 Montpellier (UM), and Terrestrial Ecology (TE)
Subjects: 0106 biological sciences, In silico, Biology, computer.software_genre, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, 18S ribosomal RNA, 03 medical and health sciences, metabrcoding, Genetics, RNA, Ribosomal, 18S, medicine, primers, Laboratorium voor Nematologie, Ecology, Evolution, Behavior and Systematics, database, 030304 developmental biology, protists, 0303 health sciences, Database, shiny, Eukaryota, Protist, Plan_S-Compliant_NO, PE&RC, Amplicon Size, 18S rRNA, PCR, international, metabarcoding, [SDE]Environmental Sciences, Primer (molecular biology), Laboratory of Nematology, computer, Biotechnology
Abstract: Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost uniquely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, a wise primer choice is needed as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few on-line resources available to list existing primers. We built a database listing 179 primers and 76 primer pairs that have been used for eukaryotic 18S rRNA metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 for eukaryotes and a subset of Silva for prokaryotes. This allowed to determine the taxonomic specificity of primer pairs, the location of mismatches as well as amplicon size. We developed a R-based web application that allows to browse the database, visualize the taxonomic distribution of the amplified sequences with the number of mismatches, and to test any user-defined primer set (https://app.pr2-primers.org). This tool will provide the basis for guided primer choices that will help a wide range of ecologists to implement protists as part of their investigations.
Published: 2021

48. Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination

Author: Luong, Ai, Adam, Hélène, Gauron, Carole, Affortit, Pablo, Ntakirutimana, Fabrice, Khong, Ngan, Le, Quang, Le, Thi, Fournel, Marie, Lebrun, Michel, Tregear, James, Jouannic, Stefan, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), LMI RICE, Agricultural Genetics Institute, Institut de Recherche pour le Développement (IRD), Hanoi University of Science and Technology (HUST), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Fondazione CariploEVOREPRICE 1201-004, CGIAR, Excellence Scholarship Program of the Embassy of France in Vietnam, ARTS program from IRD, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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: PLETHORA, rice, fungi, panicle, branching, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, yield, meristem
Abstract: International audience; Grain yield, which is one of the most important traits in rice breeding, is controlled in part by panicle branching patterns. Numerous genes involved in the control of panicle architecture have been identified through mutant and QTL characterization. Previous studies suggested the importance of several AP2/ERF transcription factor-encoding genes in the control of panicle development, including the AINTEGUMENTA/PLETHORA-like ( euANT/PLT ) genes. The ANT gene was specifically considered to be a key regulator of shoot and floral development in Arabidopsis thaliana . However, the likely importance of paralogous euANT/PLT genes in the regulation of meristem identities and activities during panicle architecture development has not to date been fully addressed in rice. In this study, we observed that the rice euANT/PLT genes displayed divergent temporal expression patterns during the branching stages of early panicle development, with spatial localization of expression in meristems for two of these genes. Moreover, a functional analysis of rice ANT -related genes using genome editing revealed their importance in the control of panicle architecture, through the regulation of axillary meristem (AM) establishment and meristem fate transition. Our study suggests that the paralogous euANT/PLT genes have become partially diversified in their functions, with certain opposing effects, since they arose from ancestral gene duplication events, and that they act in regulating the branching of the rice panicle.
Published: 2021

49. Cassava diseases caused by Xanthomonas phaseoli pv. manihotis and Xanthomonas cassavae

Author: Zárate‐Chaves, Carlos, Gómez de la Cruz, Diana, Verdier, Valérie, López, Camilo, Bernal, Adriana, Szurek, Boris, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), The Sainsbury Laboratory [Norwich] (TSL), Universidad Nacional de Colombia [Bogotà] (UNAL), Universidad de los Andes [Bogota] (UNIANDES), Challenge Research Program on RTB, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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: quantitative resistance, Xanthomonas, fungi, cassava bacterial blight, food and beverages, cassava bacterial necrosis, cassava, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; Xanthomonas phaseoli pv. manihotis (Xpm) and X. cassavae (Xc) are two bacterial pathogens attacking cassava. Cassava bacterial blight (CBB) is a systemic disease caused by Xpm, which might have dramatic effects on plant growth and crop production. Cassava bacterial necrosis is a nonvascular disease caused by Xc with foliar symptoms similar to CBB, but its impacts on the plant vigour and the crop are limited. In this review, we describe the epidemiology and ecology of the two pathogens, the impacts and management of the diseases, and the main research achievements for each pathosystem. Because Xc data are sparse, our main focus is on Xpm and CBB.
Published: 2021

50. Identifying explicit and tacit knowledge in a life science knowledge base

Author: Saoud, Johanna, Gutierrez, Alain, Huchard, Marianne, Silvie, Pierre, Martin, Pierre, Models And Reuse Engineering, Languages (MAREL), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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: ComputingMilieux_MISCELLANEOUS, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract: International audience; An alternative to the use of synthetic pesticides and antibiotics in agriculture is to spray local plants extracts, in aqueous or essential oil form. To this end, the Knomana knowledge base [1] compiles various knowledge sets on plant use such as the 42000 descriptions of pesticidal plant uses for plant, animal, and public health presented in the literature. As the One Health approach dictates to be aware of the additional uses of these pesticidal plants to prevent their unintended effects on the animal, the human, and their environment, the challenge for the domain experts (e.g. entomologist, pathologist) is thus to identify the pesticidal plants in Knomana considering the One Health approach.With the aim to present knowledge to the expert using a compact and comprehensive formalism, in [2], we computed the Duquenne-Guigues basis (DGB) of implications on an excerpt of Knomana, in which each plant is described using its taxonomy (i.e. species, genus, and family), to be consumed as food, and to be used in medical care. The DGB method is based on Formal Concept Analysis (FCA) and provides a cardinality-minimal set of non-redundant implications. By considering a reduced knowledge set, this work identifed 3 types of knowledge elements in the implications: knowledge on plant use at diverse taxonomy levels (e.g. Plants from Meliaceae family are not consumed as food), plant taxonomy (e.g. A plant from Salvia genus is from Lamiaceae family), and side effect of the knowledge set, e.g. a plant from the Piperaceae family is from the genus Piper. This latter illustration is not in accordance with taxonomic referential and thus informs on the extend of knowledge inserted in Knomana. Moreover, as plant taxonomy is known by the experts, removing it from the implications eases their reading but makes it tacit knowledge.Implementing this method to select pesticidal plants requires to consider Knomana as a multidimensional (ternary) dataset, and thus to use the extension of FCA devoted to this kind of knowledge discovery, i.e. Relational Concept Analysis (RCA). Therefore, computing the DGB of implications based on RCA provides linked set of implications which includes the existential quantifer. Converting this formulation as practical expression is a need for the domain experts.This poster describes the product line that formulates Knomana knowledge on pesticidal plants as implications, from which the implicit knowledge elements were removed and the side effects are highlighted to alert the expert. This product line was developed using the library fca4j from Cogui software (http://www.lirmm.fr/cogui/), that provides the RCA based DGB of implications, and using a post-process which differentiates the 3 types of knowledge elements within the implications. As an illustration, this poster presents the implications on Spodoptera frugiperda, a highly polyphagous insect that is close to invade South of Europe. The perspective of this work is to identify pesticidal European plants species that share chemical components similarities with plants used to control this pest in its native area.
Published: 2021

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