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1. Vector competence of sterile male Glossina fuscipes fuscipes for Trypanosoma brucei brucei: implications for the implementation of the sterile insect technique in a sleeping sickness focus in Chad

Author: Mahamat Hissene Mahamat, Adeline Ségard, Jean-Baptiste Rayaisse, Rafael Argiles-Herrero, Andrew Gordon Parker, Philippe Solano, Adly Mohamed Mohamed Abd-Alla, Jérémy Bouyer, Sophie Ravel, Institut de Recherche en Elevage pour le Developpement [N'Djamena, Tchad] (IRED), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Centre international de recherche-développement sur l'élevage en zone sub-humide (CIRDES), Insect Pest Control Laboratory (IPC laboratory), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO)-International Atomic Energy Agency [Vienna] (IAEA), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Joint FAO/IAEA Programme - Nuclear Techniques in Food and Agriculture, This work was funded by IAEA grant EVT 1804311 to Hissene Mahamat and was supported by the project, Research Infrastructures for the control of vector-borne diseases (Infravec2), which has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement number 731060., and European Project: 731060,INFRAVEC2(2017)
Subjects: Infectious Diseases, Trypanosoma brucei gambiense, [SDV]Life Sciences [q-bio], Trypanocide, Isometamidium, Parasitology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Tsetse
Abstract: Background Human African trypanosomiasis (HAT) is a neglected tropical disease caused by Trypanosoma brucei gambiense transmitted by tsetse flies in sub-Saharan West Africa. In southern Chad the most active and persistent focus is the Mandoul focus, with 98% of the reported human cases, and where African animal trypanosomosis (AAT) is also present. Recently, a control project to eliminate tsetse flies (Glossina fuscipes fuscipes) in this focus using the sterile insect technique (SIT) was initiated. However, the release of large numbers of sterile males of G. f. fuscipes might result in a potential temporary increase in transmission of trypanosomes since male tsetse flies are also able to transmit the parasite. The objective of this work was therefore to experimentally assess the vector competence of sterile males treated with isometamidium for Trypanosoma brucei brucei. Methods An experimental infection was set up in the laboratory, mimicking field conditions: the same tsetse species that is present in Mandoul was used. A T. b. brucei strain close to T. b. gambiense was used, and the ability of the sterile male tsetse flies fed on blood with and without a trypanocide to acquire and transmit trypanosomes was measured. Results Only 2% of the experimentally infected flies developed an immature infection (midgut) while none of the flies developed a metacyclic infection of T. b. brucei in the salivary glands. We did not observe any effect of the trypanocide used (isometamidium chloride at 100 mg/l) on the development of infection in the flies. Conclusions Our results indicate that sterile males of the tested strain of G. f. fuscipes were unable to cyclically transmit T. b. brucei and might even be refractory to the infection. The data of the research indicate that the risk of cyclical transmission of T. brucei by sterile male G. f. fuscipes of the strain colonized at IAEA for almost 40 years appears to be small. Graphical Abstract
Published: 2023

2. Architecture and yield relationship in hazelnut tree

Author: Grisafi, Francesca, Farinelli, Daniela, Costes, Evelyne, Boudon, Frédéric, Durand, Jean-Baptiste, Tombesi, S., Università cattolica del Sacro Cuore = Catholic University of the Sacred Heart [Roma] (Unicatt), Università degli Studi di Perugia = University of Perugia (UNIPG), 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, 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), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Serra, S., and Lauri, P.-É.
Subjects: Nut, Branching, Shoot length, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Horticulture, Corylus avellana, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, Hazel
Abstract: International audience; Yield reduction over the years is a phenomenon that affects many fruit tree species, including hazel (Corylus avellana). Studying plant architecture could provide useful information for improving crop management, such as pruning, to reduce the impact of yield reductions. This study aimed to compare the relationship between bud composition and shoot length in hazel shoots. The experiment was carried out in January 2020 and 2021 in Deruta, Perugia (Italy). In 2020, 120 1-year-old shoots of C. avellana 'Tonda di Giffoni' were sampled. In 2021, the same observations were performed on lateral and apical 1-year-old shoots that had burst from parental buds in spring 2020. Depending on its length, each shoot was sorted into four categories: short (Sh) when shorter than 5 cm, medium (Me) when between 5 and 20 cm, long (Lo) when between 20 and 40 cm, and very long (VLo) when longer than 40 cm. For each shoot, shoot length, axillary and apical bud fate was recorded at each node: vegetative bud, latent bud, catkin, and mixed bud (V, B, C, and M, respectively). Percentage of lateral mixed buds was higher in longer shoots than in shorter ones while that of vegetative buds remained constant whatever the length. Fruit set, computed as the ratio between the number of nuts and the number of mixed buds, was significantly higher in Lo and VLo shoots. It was observed that the length of lateral proleptic shoots, developed in 2021, was related to the length of the bearer shoot from which it was developed. Proleptic lateral Sh shoots were the most frequent among all length categories while longer proleptic shoots (Lo and VLo) were originated only from Lo and VLo shoots. Managing tree architecture, considering a good balance between long and short shoots, and mixed and vegetative buds, could help control and prevent yield decrease in hazelnut trees.
Published: 2023

3. A major genetic locus in neighbours controls changes of gene expression and susceptibility in intraspecific rice mixtures

Author: Rémi Pélissier, Aurélie Ducasse, Elsa Ballini, Julien Frouin, Cyrille Violle, Jean‐Benoit Morel, 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), 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, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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 Agro Montpellier, ANR-16-IDEX-0006,MUSE,MUSE(2016), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: indirect genetic effect, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, modulation of disease by neighbours, Physiology, rice, [SDV]Life Sciences [q-bio], transcriptomic, Plant Science, transcriptomic response toneighbour
Abstract: International audience; Reports indicate that intraspecific neighbours alter the physiology of focal plants, and with a few exceptions, their molecular responses to neighbours are unknown. Recently, changes in susceptibility to pathogen resulting from such interactions were demonstrated, a phenomenon called neighbour-modulated susceptibility (NMS). However, the genetics of NMS and the associated molecular responses are largely unexplored. Here, we analysed in rice the modification of biomass and susceptibility to the blast fungus pathogen in the Kitaake focal genotype in the presence of 280 different neighbours. Using genome-wide association studies, we identified the loci in the neighbour that determine the response in Kitaake. Using a targeted transcriptomic approach, we characterized the molecular responses in focal plants co-cultivated with various neighbours inducing a reduction in susceptibility. Our study demonstrates that NMS is controlled by one major locus in the rice genome of its neighbour. Furthermore, we show that this locus can be associated with characteristic patterns of gene expression in focal plant. Finally, we propose an hypothesis where Pi could play a role in explaining this case of NMS. Our study sheds light on how plants affect the physiology in their neighbourhood and opens perspectives for understanding plant-plant interactions.
Published: 2023

4. Bactrocera dorsalis in the Indian Ocean: A tale of two invasions

Author: Pablo Deschepper, Sam Vanbergen, Yue Zhang, Zhihong Li, Issa Mze Hassani, Nausheen Azhaar Patel, Henriette Rasolofoarivao, Sandeep Singh, Suk Ling Wee, Marc De Meyer, Massimiliano Virgilio, Hélène Delatte, Royal Museum for Central Africa [Tervuren] (RMCA), China Agricultural University (CAU), Institut National de la Recherche pour l'Agriculture, la Pêche et l'Environnement (INRAPE), Ministry of Agro Industry and Food Security, Partenaires INRAE, Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Punjab Agricultural University (PAU), Universiti Kebangsaan Malaysia (UKM), 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), and The authors acknowledge the Plant Protection Platform (3P, IBISA) where DNA extractions were conducted and David Nestel for providing us with samples of B. zonata. Funding for this research was provided by the EU-FF-IPM H2020 FF-IPM project (Grant ID: 818184), and the National Natural Science Foundation of China (Grant ID: 31972341). The computational resources (Stevin Supercomputer Infrastructure) and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by Ghent University, FWO, and the Flemish Government—department EWI.
Subjects: [SDV]Life Sciences [q-bio], phylogeography, invasive species, pest species, Genetics, Indian Ocean, Ecology, Evolution, Behavior and Systematics, Tephritidae, H10 - Ravageurs des plantes, Bactrocera dorsalis, General Agricultural and Biological Sciences, Génotype, Espèce envahissante
Abstract: International audience; An increasing number of invasive fruit fly pests are colonizing new grounds. With this study, we aimed to uncover the invasion pathways of the oriental fruit fly, Bactrocera dorsalis into the islands of the Indian Ocean. By using genome-wide SNP data and a multipronged approach consisting of PCA, ancestry analysis, phylogenetic inference, and kinship networks, we were able to resolve two independent invasion pathways. A western invasion pathway involved the stepping-stone migration of B. dorsalis from the east African coast into the Comoros, along Mayotte and into Madagascar with a decreasing genetic diversity. The Mascarene islands (Reunion and Mauritius), on the contrary, were colonized directly from Asia and formed a distinct cluster. The low nucleotide diversity suggests that only a few genotypes invaded the Mascarenes. The presence of many long runs of homozygosity (ROH) in the introduced populations is indicative of population bottlenecks, with evidence of a more severe bottleneck for populations along the western migration pathway than on the Mascarene islands. More strict phytosanitary regulations are recommended in order to prevent the further spread of B. dorsalis.
Published: 2022

5. Insight into the control of nodule immunity and senescence during Medicago truncatula symbiosis

Author: Fathi Berrabah, Gautier Bernal, Ait-Salem Elhosseyn, Cyrille El Kassis, Roxane L’Horset, Farouk Benaceur, Jiangqi Wen, Kirankumar S Mysore, Marie Garmier, Benjamin Gourion, Pascal Ratet, Véronique Gruber, Université Amar Telidji - Laghouat, Centre de Recherche en biotechnologie (CRBt) Constantine, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-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), Oklahoma State University [Stillwater] (OSU), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Paris Cite University, Paris Saclay University, National Science Foundation, USA (DBI 0703285 and IOS-1127155), programs for foreign researchers from Paris Cite ́ University and Paris Saclay University, ANR-15-CE20-0005,STAYPINK,Mécanismes contrôlant la transition entre fixation d'azote et sénescence dans les nodosités symbiotiques de légumineuses(2015), ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), Biology Department, Amar Telidji University, Laghouat, Algeria, Research Unit of Medicinal Plants (RUMP), This work was supported by the grant ANR-15-CE20 0005 (STAYPINK) and funding obtained from the invitation programs for foreign researchers from Paris Cite University and Paris Saclay University. This study contributes to the IdEX Universite de Paris ANR-18-IDEX-0001. Medicago truncatula Tnt1 mutants were created through research funded, in part, by grants from the National Science Foundation, USA (DBI 0703285 and IOS-1127155)., and National Science Foundation, USA (DBI 0703285 and IOS-1127155).
Subjects: Physiology, [SDV]Life Sciences [q-bio], Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Cysteine Proteases, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicago truncatula, Genetics, Symbiosis, Root Nodules, Plant, Plant Proteins, Sinorhizobium meliloti, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers: Medtr4g107930: CP3; Medtr4g079770: CP4; Medtr5g022560: CP2; Medtr4g079470: CP5; TC106667: Actine; Medtr1g099310.1: PR8; Medtr4g120970.1/Medtr6g033450.1: PR10; Medtr5g010640.1: PR5.3; Medtr8g096910.1: PR5.6; Medtr5g088770.1: PHYTOCYSTATIN32; Medtr2g026040.1: PHYTOCYSTATIN5; Medtr4g085800: DNF2; Medtr3g079850: SymCRK; MtrunA17_Chr7g0239441: RSD. Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers: Medtr4g107930: CP3; Medtr4g079770: CP4; Medtr5g022560: CP2; Medtr4g079470: CP5; TC106667: Actine; Medtr1g099310.1: PR8; Medtr4g120970.1/Medtr6g033450.1: PR10; Medtr5g010640.1: PR5.3; Medtr8g096910.1: PR5.6; Medtr5g088770.1: PHYTOCYSTATIN32; Medtr2g026040.1: PHYTOCYSTATIN5; Medtr4g085800: DNF2; Medtr3g079850: SymCRK; MtrunA17_Chr7g0239441: RSD.; International audience; Medicago (Medicago truncatula) establishes a symbiosis with the rhizobia Sinorhizobium sp, resulting in the formation of nodules where the bacteria fix atmospheric nitrogen. The loss of immunity repression or early senescence activation compromises symbiont survival and leads to the formation of nonfunctional nodules (fix−). Despite many studies exploring an overlap between immunity and senescence responses outside the nodule context, the relationship between these processes in the nodule remains poorly understood. To investigate this phenomenon, we selected and characterized three Medicago mutants developing fix− nodules and showing senescence responses. Analysis of specific defense (PATHOGENESIS-RELATED PROTEIN) or senescence (CYSTEINE PROTEASE) marker expression demonstrated that senescence and immunity seem to be antagonistic in fix− nodules. The growth of senescence mutants on non-sterile (sand/perlite) substrate instead of sterile in vitro conditions decreased nodule senescence and enhanced defense, indicating that environment can affect the immunity/senescence balance. The application of wounding stress on wild-type (WT) fix+ nodules led to the death of intracellular rhizobia and associated with co-stimulation of defense and senescence markers, indicating that in fix+ nodules the relationship between the two processes switches from opposite to synergistic to control symbiont survival during response to the stress. Our data show that the immune response in stressed WT nodules is linked to the repression of DEFECTIVE IN NITROGEN FIXATION 2 (DNF2), Symbiotic CYSTEINE-RICH RECEPTOR-LIKE KINASE (SymCRK), and REGULATOR OF SYMBIOSOME DIFFERENTIATION (RSD), key genes involved in symbiotic immunity suppression. This study provides insight to understand the links between senescence and immunity in Medicago nodules. Analyses of Medicago mutants with non-functional nodules highlight the relationship and mechanisms controlling the establishment of the immune and senescence programs during nodule organogenesis.
Published: 2022

6. Vaccine efficacy trials for Crimean-Congo haemorrhagic fever: Insights from modelling different epidemiological settings

Author: Juan F Vesga, Raphaёlle Métras, Madeleine H A Clark, Edris Ayazi, Andrea Apolloni, Toby Leslie, Veerle Msimang, Peter N. Thompson, W John Edmunds, London School of Hygiene and Tropical Medicine (LSHTM), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Ministry of Public Health [Afghanistan], Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), University of Pretoria [South Africa], National Institute for Communicable Diseases [Johannesburg] (NICD), W.J.E., JFV and MHAC were funded by the Department of Health and Social Care using UK Aid funding managed by the National Institute for Health Research (Vaccine Efficacy Evaluation for Priority Emerging Diseases: PR-OD-1017-20002)., and LESUR, Hélène
Subjects: Vaccines, Livestock, Mathematical modelling, General Veterinary, General Immunology and Microbiology, [SDV]Life Sciences [q-bio], Public Health, Environmental and Occupational Health, Vaccine Efficacy, [SDV] Life Sciences [q-bio], Clinical trials, Infectious Diseases, Hemorrhagic Fever Virus, Crimean-Congo, Animals, Humans, Molecular Medicine, Hemorrhagic Fever, Crimean, Crimean-Congo haemorrhagic fever
Abstract: BackgroundCrimean-Congo haemorrhagic fever (CCHF) is a priority emerging pathogen for which a licensed vaccine is not yet available. We aim to assess the feasibility of conducting phase III vaccine efficacy trials and the role of varying transmission dynamics.MethodsWe calibrate models of CCHF virus (CCHFV) transmission among livestock and spillover to humans in endemic areas in Afghanistan, Turkey and South Africa. We propose an individual randomised controlled trial targeted to high-risk population, and use the calibrated models to simulate trial cohorts to estimate the minimum trial endpoints necessary to analyse vaccine efficacy, sample size and follow-up time in the three settings.ResultsUnder assumptions of a minimum vaccine efficacy of 60%, the minimum sample size needed to accrue the required 150 clinical endpoints in a minimum follow-up time of 6 months is estimated to be 34,000 (CrI 95%, 16,750 – 88,725) and 37,000 (CrI 95%, 13,000 – 77,250) in Afghanistan and Turkey, respectively. The results suggest that for South Africa the low endemic transmission levels will not permit achieving the necessary conditions for conducting this trial within a realistic follow-up time. In a scenario of CCHFV infection (rather than clinical case) as trial endpoint, the required sample size is reduced by 70% to 80% in Afghanistan and Turkey, and in South Africa, a trial becomes feasible for large sample sizes (>75,000) and vaccine efficacy of >70%. Increased expected vaccine efficacy >60% will reduce the required number of trial endpoints and thus the sample size and follow-time in phase III trials.ConclusionsUnderlying endemic transmission levels will play a central role in defining the feasibility of phase III vaccine efficacy trials. Endemic settings in Afghanistan and Turkey offer conditions under which such studies could feasibly be conducted.
Published: 2022

7. The GeoLifeCLEF 2023 Dataset to evaluate plant species distribution models at high spatial resolution across Europe

Author: Botella, Christophe, Benjamin, Deneu, Diego Gonzalez, Marcos, Maximilien, Servajean, Théo, Larcher, Joaquim, Estopinan, César, Leblanc, Bonnet, Pierre, Joly, Alexis, Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-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), ADVanced Analytics for data SciencE (ADVANSE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université Paul-Valéry - Montpellier 3 (UPVM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), European Project: 101060693,GUARDEN, and European Project: 101060639,MAMBO
Subjects: Europe, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Presence-only, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], SDM, Deep SDM, prediction, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Remote sensing, Presence-absence, Species distribution, species assemblages, biodiversity
Abstract: The full dataset is freely available at the link below (perennial repository) for academic use or other non-commercial use: https://lab.plantnet.org/seafile/d/936fe4298a5a4f4c8dbd/; The difficulty to measure or predict species community composition at fine spatio-temporal resolution and over large spatial scales severely hampers our ability to understand species assemblages and take appropriate conservation measures. Despite the progress in species distribution modeling (SDM) over the past decades, SDM are just beginning to integrate high resolution remote sensing data and their predictions are still entailed by the many biases and heterogeneous quality of the available biodiversity observations, most often opportunistic presence only data. We designed a European scale dataset covering around 10K plant species to calibrate and evaluate SDM predictions of species composition in space and time at high spatial resolution (~10m), and study their spatial transferability. For model training, we extracted and harmonized 5 million heterogeneous presence-only observations from selected GBIF datasets and 5 thousand exhaustive presence-absence surveys both sampled during the 2017-2021. We associated them to various environmental rasters classically used in SDMs, as well as to 10x10m resolution RGB and Near-Infra-Red satellite images and 20 years-time series of climatic variables and satellite point values. The evaluation dataset is based on 20K standardized presence-absence surveys separated from the training set with a spatial block hold out procedure. The GeoLifeCLEF 2023 dataset is open access and the first benchmark for researchers aiming to improve the prediction of plant species composition at a very fine spatial grain and at continental scale. It is also a space to explore new ways of combining massive and diverse species observations with environmental information at various scales. Innovative AI-based approaches, in particular, should be among the most interesting methods to experiment with on the GeoLifeCLEF 2023 dataset.
Published: 2023

8. The GeoLifeCLEF 2023 Dataset to evaluate plant species distribution models at high spatial resolution across Europe

Author: Botella, Christophe, Deneu, Benjamin, Diego Gonzalez, Marcos, Servajean, Maximilien, Larcher, Théo, Estopinan, Joaquim, Leblanc, César, Bonnet, Pierre, Joly, Alexis, Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-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), ADVanced Analytics for data SciencE (ADVANSE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université Paul-Valéry - Montpellier 3 (UPVM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), European Project: 101060693,GUARDEN, and European Project: 101060639,MAMBO
Subjects: Europe, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Presence-only, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], SDM, Deep SDM, prediction, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Remote sensing, Presence-absence, Species distribution, species assemblages, biodiversity
Abstract: The full dataset is freely available at the link below (perennial repository) for academic use or other non-commercial use: https://lab.plantnet.org/seafile/d/936fe4298a5a4f4c8dbd/; The difficulty to measure or predict species community composition at fine spatio-temporal resolution and over large spatial scales severely hampers our ability to understand species assemblages and take appropriate conservation measures. Despite the progress in species distribution modeling (SDM) over the past decades, SDM are just beginning to integrate high resolution remote sensing data and their predictions are still entailed by the many biases and heterogeneous quality of the available biodiversity observations, most often opportunistic presence only data. We designed a European scale dataset covering around 10K plant species to calibrate and evaluate SDM predictions of species composition in space and time at high spatial resolution (~10m), and study their spatial transferability. For model training, we extracted and harmonized 5 million heterogeneous presence-only observations from selected GBIF datasets and 5 thousand exhaustive presence-absence surveys both sampled during the 2017-2021. We associated them to various environmental rasters classically used in SDMs, as well as to 10x10m resolution RGB and Near-Infra-Red satellite images and 20 years-time series of climatic variables and satellite point values. The evaluation dataset is based on 20K standardized presence-absence surveys separated from the training set with a spatial block hold out procedure. The GeoLifeCLEF 2023 dataset is open access and the first benchmark for researchers aiming to improve the prediction of plant species composition at a very fine spatial grain and at continental scale. It is also a space to explore new ways of combining massive and diverse species observations with environmental information at various scales. Innovative AI-based approaches, in particular, should be among the most interesting methods to experiment with on the GeoLifeCLEF 2023 dataset.
Published: 2023

9. Deciphering plant resilience mechanisms to face the multiple disease challenge in fruit trees

Author: Serrie, Marie, Ribeyre, Fabienne, Brun, Laurent, Audergon, Jean-Marc, Quilot-Turion, Bénédicte, Roth, Morgane, Génétique et Amélioration des Fruits et Légumes (GAFL), 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), Unité Expérimentale de Recherches Intégrées en Production Fruitière (UERI), Agropolis Fundation (ID 2002-230)BAP INRAE Department, Maud Tenaillon, and Christophe Robaglia
Subjects: Disease resilience, Plant immunity, Sustainability, Biotic stress, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Multi-disease challenge, Fruit trees, Biomarkers
Abstract: International audience; As perennial plants, fruit trees must cope, individually, with the fluctuating threat of multiple pathogens over the years. In this long-lasting battle for plant immunity, disease resilience is emerging as a key mechanism for tree survival and fitness. More fundamental research is required to improve our understanding of disease resilience mechanisms, which in turn could be particularly relevant for a more sustainable fruit production. As this approach is novel for that field, we propose i) a clear definition of resilience for fruit producing trees, ii) a methodology for studying its phenotypic components which requires repeated measures of “resilience biomarkers”, iii) to decipher the genetic architecture of resilience components, and iv) an innovative strategy based on high-throughput phenotyping and genomics for identifying resilient genotypes. All in all, disease resilience appears as a meaningful breeding perspective in a context of unprecedented plant protection restrictions.
Published: 2023

10. Spatio-temporal analysis of strawberry architecture: insights into the control of branching and inflorescence complexity

Author: Marc Labadie, Karine Guy, Marie-Noëlle Demené, Yves Caraglio, Gaetan Heidsieck, Amelia Gaston, Christophe Rothan, Yann Guédon, Christophe Pradal, Béatrice Denoyes, 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, 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), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Invenio, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: plant architecture, Physiology, OpenAlea, [SDV]Life Sciences [q-bio], branching, multiscale tree graph, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Science, Fragaria × ananassa, hidden hybrid Markov/semi-Markov chain
Abstract: Plant architecture plays a major role in flowering and therefore in crop yield. Attempts to visualize and analyse strawberry plant architecture have been few to date. Here, we developed open-source software combining two- and three-dimensional representations of plant development over time along with statistical methods to explore the variability in spatio-temporal development of plant architecture in cultivated strawberry. We applied this software to six seasonal strawberry varieties whose plants were exhaustively described monthly at the node scale. Results showed that the architectural pattern of the strawberry plant is characterized by a decrease of the module complexity between the zeroth-order module (primary crown) and higher-order modules (lateral branch crowns and extension crowns). Furthermore, for each variety, we could identify traits with a central role in determining yield, such as date of appearance and number of branches. By modeling the spatial organization of axillary meristem fate on the zeroth-order module using a hidden hybrid Markov/semi-Markov mathematical model, we further identified three zones with different probabilities of production of branch crowns, dormant buds, or stolons. This open-source software will be of value to the scientific community and breeders in studying the influence of environmental and genetic cues on strawberry architecture and yield.
Published: 2023

11. Rethinking Iconic Species Reforestation in West Africa: Seed Shape Harnessing Is Strategic for Enhanced Germination and Vigorous Growth in Khaya senegalensis and Parkia biglobosa

Author: Adji, Beda, Letort, Véronique, Wang, Xiujuan, Kang, Mengzhen, de Reffye, Philippe, Jaeger, Marc, Cilas, Christian, Kouassi, Kouadio, Duminil, Jérôme, Sabatier, Sylvie, Akaffou, Doffou, Université Jean Lorougnon Guédé (UJloG ), Mathématiques et Informatique pour la Complexité et les Systèmes (MICS), CentraleSupélec-Université Paris-Saclay, Chinese Academy of Sciences [Beijing] (CAS), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), AMAP Lab [Saint-Pierre - La réunion], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Cirad Direction Générale (Cirad-DG), Diversité, adaptation, développement des plantes (UMR DIADE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)
Subjects: Khaya senegalensis, Côte d'Ivoire, [SDE]Environmental Sciences, Parkia biglobosa, seed quality, reforestation, seed quality reforestation Khaya senegalensis Parkia biglobosa Côte d'Ivoire
Abstract: International audience; Seed size is a critical factor that can impact the regeneration process of plant populations. The objective of this study is to identify optimal seeds for the cultivation of two overexploited native forest species in Côte d'Ivoire, namely Khaya senegalensis (Desr.) A.Juss., 1830 and Parkia biglobosa (Jacq.) R.BR. ex G. Don, 1830. A total of 1080 seeds per species were evaluated for germination and seedling vigour in two distinct environments (dry and humid) in Côte d'Ivoire. The results demonstrated that, for Khaya senegalensis, larger seeds exhibited higher germination rates, whereas for Parkia biglobosa, smaller and medium-sized seeds showed better germination performance. However, regardless of species and study site, larger seeds consistently produced more vigorous seedlings. In this case, pretreatment tests on large seeds of Parkia biglobosa can potentially enhance their germination performance. Large seeds, ranging from 0.25-0.37 g in Khaya senegalensis and 0.2-0.32 g in Parkia biglobosa, appear to be the most suitable and best candidates for high-quality, high-performance seeds to optimise the cultivation of these species in Côte d'Ivoire. Distributing such seeds to farmers can contribute to the success of reforestation and agroforestry programs involving these target species in Côte d'Ivoire. These findings contribute to the sustainable management of the target species and can serve as a basis for restructuring forest regeneration policies in Côte d'Ivoire.
Published: 2023

12. About sterile insect control strategies in a two patches system

Author: Dumont, Yves, Duprez, Michel, Privat, Yannick, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), AMAP Lab [Saint-Pierre - La réunion], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Mathematics and Applied Mathematics, University of Pretoria, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Computational Anatomy and Simulation for Medicine (MIMESIS), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Institut de Recherche Mathématique Avancée (IRMA), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France (IUF), and Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.)
Subjects: metapopulation model, optimal control, Bactrocera dorsalis, Control strategies, Sterile Insect Technique, monotone cooperative system, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], biological control, patches
Abstract: International audience; Sterile Insect Technique is an autocidal method to control Vector of diseases and crop pest. It consists of releasing males sterilized by ionization, in a targeted area, that will mate with the wild females, resulting in a reduce, eventually a local elimination, of the wild population. However, migration of wild insects, from a non-targeted area, can be problematic and reduce the efficiency of SIT [1]. The control strategies should be adapted to take this issue into account. We consider a two patches system, where Patch 1 is the targeted area linked to another area, Patch 2, that needs not to be controlled. Wild and sterile insects can circulate between the two Patches, so that different issues have to be solved. Is it possible to find one or several strategies, and among them an optimal strategy, to reach elimination in patch 1? Should we control both patches? Using results related to monotone cooperative systems [2] and also tools from optimal control theory, we will show some theoretical responses [3]. We will also illustrate the theoretical results with numerical simulations and discuss the extension of our results.
Published: 2023

13. Late Cenozoic environmental changes drove the diversification of a weevil genus endemic to the Cape Floristic Region

Author: Noémie M.‐C. Hévin, Steffan Hansen, Pia Addison, Laure Benoit, Gael J. Kergoat, Julien Haran, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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, 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 de Poitiers, Stellenbosch University, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and The first author was supported by a grant from the CBGP laboratory (Montpellier, France) for her Master's degree.
Subjects: biodiversity hotspot, Phlyctinus callosus, [SDV]Life Sciences [q-bio], Genetics, Entiminae, Animal Science and Zoology, sea level oscillations, banded fruit weevil, Molecular Biology, Ecology, Evolution, Behavior and Systematics, allopatric speciation
Abstract: We thank the Western Cape Nature Conservation Board (permit No. CN44-30-4229), the Cape Research Centre (South African National Parks, CRC/2019-2020/012-2012/V1) and Grootbos Private Nature reserve for authorization to collect specimens in the Western Cape province of South Africa.; International audience; The Cape Floristic Region in the Republic of South Africa is a well-recognized hotspot of biodiversity. Although this region is mostly known for its high level of plant diversity and endemicity, it also hosts an understudied and likely diverse arthropod fauna. Here we investigate the evolutionary history and timing of diversification of the apterous weevil genus Phlyctinus (Curculionidae: Entiminae), which is endemic to the coastal area and adjacent mountain ranges of the Cape floristic region and generally associated with sunflower plants (Asteraceae). We use a diverse array of molecular analyses (phylogenetic inference, molecular species delimitation and dating analyses) to analyse a novel molecular dataset of 202 weevil specimens (including 170 Phlyctinus sampled in 60 sites), and sequenced for two mitochondrial and four nuclear gene fragments. Phylogenetic and dating analyses indicate that the genus started diversifying in the late Miocene, with contrasting diversification dynamics for the three inferred clades, which present disjunct distributions. Host plant records and the lack of relatedness of species living in sympatry indicate that the diversification of Phlyctinus was predominantly driven by allopatric (geographic) speciation. We hypothesize that the interplay between topography and recurring cycles of coastline-habitat fragmentation resulting from sea level oscillations spurred the diversification of the most speciose clade, whereas in the two remaining clades populations likely remained connected thus hampering allopatric speciation. Interestingly, this pattern echoes with the role of sea level oscillations as an important driver of the radiation of several lineages in the coastline ecosystems of the Cape Floristic Region.
Published: 2022

14. Tannin phenotyping of the Vitaceae reveals a phylogenetic linkage of epigallocatechin in berries and leaves

Author: Jean-Marc Brillouet, Charles Romieu, Roberto Bacilieri, Peter Nick, Anna Trias-Blasi, Erika Maul, Katalin Solymosi, Peter Teszlák, Jiang-Fu Jiang, Lei Sun, Danielle Ortolani, Jason P Londo, Ben Gutierrez, Bernard Prins, Marc Reynders, Frank Van Caekenberghe, David Maghradze, Cecile Marchal, Amir Sultan, Jean-Francois Thomas, Daniel Scherberich, Helene Fulcrand, Laurent Roumeas, Guillaume Billerach, Vugar Salimov, Mirza Musayev, Muhammad Ejaz Ul Islam Dar, Jean-Benoit Peltier, Michel Grisoni, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), 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), 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, Karlsruhe Institute of Technology (KIT), Royal Botanic Gardens [Kew], Julius Kühn-Institut (JKI), Eötvös Loránd University (ELTE), Department of Plant Anatomy, Institute of Biology [Budapest], Faculty of Sciences [Budapest], Eötvös Loránd University (ELTE)-Eötvös Loránd University (ELTE)-Faculty of Sciences [Budapest], Eötvös Loránd University (ELTE)-Eötvös Loránd University (ELTE), University of Pecs, Chinese Academy of Agricultural Sciences (CAAS), Jardin Exotique, USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service, University of California [Davis] (UC Davis), University of California (UC), Meise Botanic Garden [Belgium] (Plantentuin), National Wine Agency of Georgia, Domaine expérimental de Vassal (MONTP DOM VASSAL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Herbarium (Stewart Collection), Jardin Botanique de Lyon, Partenaires INRAE, Azerbaijani Scientific Research Institute of Viticulture and Winemaking, Azerbaijan National Academy of Sciences (ANAS), University of Azad Jammu & Kashmir (UAJ&K), Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: American wild grapevines, leaf, phenotype, [SDV]Life Sciences [q-bio], leaf margin teeth, Original Articles, Plant Science, Asian wild grapevines, Catechin, Plant Leaves, Vitaceae, Vitis vinifera, Fruit, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Condensed tannins, pericarp, Proanthocyanidins, Vitis, epigallocatechin, Tannins, EGC(-) vines, Phylogeny, EGC(+) vines
Abstract: Background and Aims Condensed tannins, responsible for berry and wine astringency, may have been selected during grapevine domestication. This work examines the phylogenetic distribution of condensed tannins throughout the Vitaceae phylogenetic tree. Methods Green berries and mature leaves of representative true-to-type members of the Vitaceae were collected before ‘véraison’, freeze-dried and pulverized, and condensed tannins were measured following depolymerization by nucleophilic addition of 2-mercaptoethanol to the C4 of the flavan-3-ol units in an organic acidic medium. Reaction products were separated and quantified by ultrahigh pressure liquid chromatography/diode array detection/mass spectrometry. Key Results and Conclusions The original ability to incorporate epigallocatechin (EGC) into grapevine condensed tannins was lost independently in both the American and Eurasian/Asian branches of the Vitaceae, with exceptional cases of reversion to the ancestral EGC phenotype. This is particularly true in the genus Vitis, where we now find two radically distinct groups differing with respect to EGC content. While Vitis species from Asia are void of EGC, 50 % of the New World Vitis harbour EGC. Interestingly, the presence of EGC is tightly coupled with the degree of leaf margin serration. Noticeably, the rare Asian EGC-forming species are phylogenetically close to Vitis vinifera, the only remnant representative of Vitis in Eurasia. Both the wild ancestral V. vinifera subsp. sylvestris as well as the domesticated V. vinifera subsp. sativa can accumulate EGC and activate galloylation biosynthesis that compete for photoassimilates and reductive power.
Published: 2022

15. In situ dynamic rheological analysis of raw yam tubers: a potential phenotyping tool for quality evaluation

Author: Bolanle Omolara Otegbayo, Thierry Tran, Julien Ricci, Olivier Gibert, Bowen University, 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)-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 Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Tropical Soil Biology and Fertility Institute of CIAT (TSBF), International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), 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, Département Systèmes Biologiques (Cirad-BIOS), Agropolis Fondation, and Bill & Melinda Gates Foundation 363 (BMGF)INV-008567
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Nutrition and Dietetics, Dioscorea, [SDV]Life Sciences [q-bio], viscoelastic properties, consumer preferences, Agronomy and Crop Science, high-throughput screening, efficient breeding, Food Science, Biotechnology
Abstract: Background: Most rheological analyses in yam have been done on starch gels, which requires starch extraction from the tubers. In situ rheology bypasses the need of starch extraction and relies on the original cell structure and complex matrix organization under stress or strain. Dynamic rheological properties of tuber from 16 accessions belonging to four yam species (Dioscorea rotundata, D. alata. D. bulbifera and D. dumetorum) were investigated for potential use as a medium throughput phenotyping screening tool that can indicate the quality of yam food products or their industrial potentials. Results: Rheographs of the tubers illustrated differences in the structure of D. bulbifera compared to other yam species. High initial storage modulus (G′) of yam parenchyma indicated tubers with strong and rigid structure which do not lose their structural integrity easily on heating. Dioscorea rotundata and D. alata varieties exhibited a lower temperature at which gelatinization took place (Tgel) equivalent to the irreversible transition during starch gelatinization (75.3 and 79.8 °C) and took shorter time (867 and 958 s, respectively) to reach the G′ maximum, compared to other species. The stress relaxation test showed that the higher the dry matter of the tubers, the higher the work to rupture the structure. Conclusion: Rheological characteristics G′, loss modulus (G″), swelling capacity and Tgel showed potential as suitable quality indicators for yam products. In situ rheological characterization of yam tubers could be used as an instrumental screening tool to phenotype for quality in yam products. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Published: 2023

16. pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex pipiens and Culex quinquefasciatus mosquitoes worldwide

Author: Amani Ghousein, Jordan Tutagata, Hans Schrieke, Manuel Etienne, Victor Chaumeau, Sebastien Boyer, Nonito Pages, David Roiz, A. Murat Eren, Guillaume Cambray, Julie Reveillaud, Biothérapies des maladies génétiques et cancers, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), 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), Centre de Démoustication, Conseil Général de Martinique, Shoklo Malaria Research Unit [Mae Sot, Thailand] (SMRU), Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford-Mahidol University [Bangkok]-Wellcome Trust-University of Oxford-Mahidol University [Bangkok]-Wellcome Trust, Centre for Tropical Medicine and Global Health [Oxford, UK], Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford-University of Oxford, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Marine Biological Laboratory, Woods Hole, Massachusetts, USA, Centre de Biologie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)
Subjects: [SDV]Life Sciences [q-bio], General Medicine
Abstract: Mosquitoes represent the most important pathogen vectors and are responsible for the spread of a wide variety of poorly treatable diseases. Wolbachia are obligate intracellular bacteria that are widely distributed among arthropods and collectively represents one of the most promising solutions for vector control. In particular, Wolbachia has been shown to limit the transmission of pathogens, and to dramatically affect the reproductive behavior of their host through its phage WO. While much research has focused on deciphering and exploring the biocontrol applications of these WO-related phenotypes, the extent and potential impact of the Wolbachia mobilome remain poorly appreciated. Notably, several Wolbachia plasmids, carrying WO-like genes and Insertion Sequences (IS), thus possibly interrelated to other genetic units of the endosymbiont, have been recently discovered. Here we investigated the diversity and biogeography of the first described plasmid of Wolbachia in Culex pipiens (pWCP) in several islands and continental countries around the world—including Cambodia, Guadeloupe, Martinique, Thailand, and Mexico—together with mosquito strains from colonies that evolved for 2 to 30 years in the laboratory. We used PCR and qPCR to determine the presence and copy number of pWCP in individual mosquitoes, and highly accurate Sanger sequencing to evaluate potential variations. Together with earlier observation, our results show that pWCP is omnipresent and strikingly conserved among Wolbachia populations within mosquitoes from distant geographies and environmental conditions. These data suggest a critical role for the plasmid in Wolbachia ecology and evolution, and the potential of a great tool for further genetic dissection and possible manipulation of this endosymbiont.
Published: 2023

17. Spatial spread of infectious diseases with conditional vector preferences

Author: Hamelin, Frédéric, Hilker, Frank M., Dumont, Yves, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), Universität Osnabrück - Osnabrück University, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), AMAP Lab [Saint-Pierre - La réunion], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), University of Pretoria [South Africa], Sergey Petrovskii (University of Leicester), Jean-Christophe Poggiale (Aix-Marseille Université), and Suzanne Touzeau (INRAE Sophia Antipolis)
Subjects: Front reversal, Monostable traveling wave, Traveling wave solution, Bistable traveling wave, [SDE]Environmental Sciences, Backward bifurcation, Monotone system, Vector preference, [MATH]Mathematics [math], Partial differential equations
Abstract: International audience; We explore the spatial spread of vector-borne infections with conditional vector preferences, meaning that vectors do not visit hosts at random. Vectors may be differentially attracted toward infected and uninfected hosts depending on whether they carry the pathogen or not. The model is expressed as a system of partial differential equations with vector diffusion. We first study the diffusion-less model. We show that conditional vector preferences alone (in the absence of any epidemiological feedback on their population dynamics) may result in bistability between the disease-free equilibrium and an endemic equilibrium. A backward bifurcation may allow the disease to persist even though its basic reproductive number is less than one. Bistability can occur only if both infected and uninfected vectors prefer uninfected hosts. Back to the model with diffusion, we show that bistability in the local dynamics may generate travelling waves with either positive or negative spreading speeds, meaning that the disease either invades or retreats into space. In the monostable case, we show that the disease spreading speed depends on the preference of uninfected vectors for infected hosts but not on the preference of infected vectors for uninfected hosts. We discuss the implications of our results for vector-borne plant diseases, which are the main source of evidence for conditional vector preferences so far.
Published: 2023

18. <scp> restoptr </scp> : an R package for ecological restoration planning

Author: Dimitri Justeau‐Allaire, Jeffrey O. Hanson, Guillaume Lannuzel, Philippe Vismara, Xavier Lorca, Philippe Birnbaum, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Carleton University, New Caledonia Plant Red List Authority Endemia, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), Agents, Apprentissage, Contraintes (COCONUT), 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), Centre Génie Industriel (CGI), IMT École nationale supérieure des Mines d'Albi-Carmaux (IMT Mines Albi), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: Wildlife corridors, Connectivity, [SPI]Engineering Sciences [physics], Ecology, Fragmentation, Systematic conservation planning, R package, Constraint programming, Landscape indices, Ecological restoration planning, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract: International audience; Ecological restoration is essential to curb the decline of biodiversity and ecosystems worldwide. Since the resources available for restoration are limited, restoration efforts must be cost-effective to achieve conservation outcomes. Although decision support tools are available to aid in the design of protected areas, little progress has been made to provide such tools for restoration efforts. Here, we introduce the restoptr R package, a decision support tool designed to identify priority areas for ecological restoration. It uses constraint programming – an artificial intelligence technique – to identify optimal plans given ecological and socio-economic constraints. Critically, it can identify strategic locations to enhance connectivity and reduce fragmentation across a broader landscape using complex landscape metrics. We illustrate its usage with a case study in New Caledonia. By applying this tool, we identified priority areas for restoration that could reverse forest fragmentation induced by mining activities in a specific area. We also found that relatively small investments could deliver large returns to restore connectivity. The restoptr R package is a free and open-source decision support tool available on the Comprehensive R Archive Network (https://cran.r-project.org/package=restoptr)
Published: 2023

19. Habitat mosaic as a driver of the resilience of native species: The case of the assemblage of small mammals from the city of Franceville, Gabon

Author: J. B. Mangombi‐Pambou, O. Fossati‐Gaschignard, N. N'Dilimabaka, O. Banga Mve‐Ella, N. M. Longo Pendy, S. E. Dibakou, O. Mediannikov, F. Fenollar, E. Leroy, M. Bourgarel, Centre International de Recherches Médicales de Franceville (CIRMF), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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, 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 des Sciences et Techniques de Masuku (USTM), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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: urban rodents, [SDV]Life Sciences [q-bio], habitat gradient, central African city, Animal Science and Zoology, community composition, landscape heterogeneity, Ecology, Evolution, Behavior and Systematics, introduced rodents
Abstract: International audience; Rodents (Rodentia) are the most abundant and diverse order of mammals, present in all habitats, including urban areas. The traffic linked to globalisation has favoured their involvement in biological invasions that have an impact on local biodiversity, the economy and human health. In Franceville, Gabon, little is known about the rodent community. We therefore studied the composition and distribution of rodents along a gradient highlighting the heterogeneity of the city's landscape. The three habitat types studied showed no difference in small mammal abundance, while the diversity index was higher in the vegetated habitat (SDI = 0.73) compared to the outdoor (SDI = 0.71) and indoor (SDI = 0.45) habitats. Our work shows the importance of vegetal remnants in the city for the maintenance of native species. It also highlights the impact of introduced species on small mammal assemblages and the need for management to reduce the factors of their proliferation.
Published: 2023

20. Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: The case of Pseudocercospora fijiensis invasion in Africa

Author: A. Gilabert, A. Rieux, S. Robert, R. Vitalis, M.‐F. Zapater, C. Abadie, J. Carlier, V. Ravigné, 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, 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), 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), 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, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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, This work was supported by the Région Languedoc-Roussillon, the Agence Nationale de la Recherche (project EMERFUNDIS ANR 07-BDIV-003 and EMILE ANR 09-BLAN-0145-01), and French Agropolis Fondation (Labex Agro – Montpellier, BIOFIS project number 1001-001 and Labex Agro –Montpellier, E-SPACE project number 1504-004). VR was funded by the European Union (European Regional Development Fund, ERDF contract GURDT I2016-1731-0006632), the Conseil Régional de La Réunion, and the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)., ANR-07-BDIV-0003,EMERFUNDIS,Comprendre les émergences de maladies fongiques de plantes : vers une estimation des risques liés aux changements globaux(2007), ANR-09-BLAN-0145,EMILE,Etude de Méthodes Inférentielles et Logiciels pour l'Evolution(2009), and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: Ecology, Approximate Bayesian Computation, population genetics, emerging disease, random forest, Ecology, Evolution, Behavior and Systematics, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Nature and Landscape Conservation
Abstract: Data were produced through the molecular genetic analysis technical facilities of the IFR119 with the help of E. Desmarais and F. Cerqueira. Bioinformatics analyses were performed using the Core Cluster of the Institut Français de Bioinformatique, the MESO@LR-Platform at the University of Montpellier and the INRAE MIGALE bioinformatics facility (doi: 10.15454/1.5572390655343293E12).The microsatellite dataset, template files for Fastsimcoal analyses and R scripts used to generate the tables and figures of the manuscript are deposited in the dryad repository (doi:10.5061/dryad.rn8pk0pgw).; International audience; The reconstruction of geographic and demographic scenarios of dissemination for invasive pathogens of crops is a key step toward improving the management of emerging infectious diseases. Nowadays, the reconstruction of biological invasions typically uses the information of both genetic and historical information to test for different hypotheses of colonization. The Approximate Bayesian Computation framework and its recent Random Forest development (ABC-RF) have been successfully used in evolutionary biology to decipher multiple histories of biological invasions. Yet, for some organisms, typically plant pathogens, historical data may not be reliable notably because of the difficulty to identify the organism and the delay between the introduction and the first mention. We investigated the history of the invasion of Africa by the fungal pathogen of banana Pseudocercospora fijiensis, by testing the historical hypothesis against other plausible hypotheses. We analyzed the genetic structure of eight populations from six eastern and western African countries, using 20 microsatellite markers and tested competing scenarios of population foundation using the ABC-RF methodology. We do find evidence for an invasion front consistent with the historical hypothesis, but also for the existence of another front never mentioned in historical records. We question the historical introduction point of the disease on the continent. Crucially, our results illustrate that even if ABC-RF inferences may sometimes fail to infer a single, well-supported scenario of invasion, they can be helpful in rejecting unlikely scenarios, which can prove much useful to shed light on disease dissemination routes.
Published: 2023

21. Using anticipation to unveil drivers of local livelihoods in Transfrontier Conservation Areas: A call for more environmental justice

Author: Robin Bourgeois, Chloé Guerbois, Nicia Giva, Prisca Mugabe, Billy Mukamuri, Richard Fynn, William’s Daré, Moseki Motsholapheko, Lerato Nare, Etienne Delay, Raphaëlle Ducrot, Joaquim Bucuane, Sara Mercandalli, Christophe Le Page, Alexandre Caron, Acteurs, Ressources et Territoires dans le Développement (UMR ART-Dev), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Paul-Valéry - Montpellier 3 (UPVM)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Nelson Mandela University [Port Elizabeth], Reconciling Ecological and Human Adaptations for Biosphere Sustainability (REHABS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Nelson Mandela University [Port Elizabeth], Eduardo Mondlane University, University of Zimbabwe (UZ), University of Botswana, Savoirs, ENvironnement et Sociétés (SENS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut de Recherche pour le Développement (IRD), National University of Science and Technology [Bulawayo], Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-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), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), European Commission, Grant/Award Number: FED/2017/394-443, Université Eduardo Mondlane, This article was supported by the EU funded ‘ProSuLi in TFCAs’ project (FED/2017/394-443) and implemented within the framework of the research platform RP-PCP (www.rp-pcp.org)., and European Project: FED/2017394-443
Subjects: southern Africa, governance, well-being, [SDE]Environmental Sciences, local communities, participatory approach, futures, protected areas, recognition justice, [SDE.ES]Environmental Sciences/Environmental and Society, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Calling on the concept of environmental justice in its distributive, procedural and recognition dimensions, we implemented a coelaborative scenario building approach to explore sustainable livelihoods pathways in four sites belonging to two Transfrontier Conservation Areas (TFCAs) in southern Africa. Grounded on participation and transdisciplinarity, as a foundation for decolonised anticipatory action research, we aimed at stimulating knowledge exchange and providing insights on the future of local livelihoods engaging experts living within these TFCAs. Our results show that wildlife and wildlife-related activities are not seen as the primary drivers of local livelihoods, despite the focus and investments of dominant stakeholders in these sectors. Instead, local governance and land use regulations emerged as key drivers in the four study sites. The state of natural resources, including water, and appropriate farming systems also appeared critical to sustain future livelihoods in TFCAs, together with the recognition of indigenous culture, knowledge and value systems. Nature conservation, especially in Africa, is rooted in its colonial past and struggles to free or decolonise itself from the habits of this past despite decades of reconsideration. To date, the enduring coloniality of conservation prevents local citizens from truly participating in the planning and designing of the TFCAs they live in, leaving room for limited benefits to local citizens and often limiting Indigenous people's capacity to conserve. A practical way forward is to consider environmental justice as a cement between the two pillars of the TFCA concept, that is, nature conservation and socio-economic development of local or neighbouring communities, as part of a more broadly and urgent need to rethink the relationships between people in, and with, the rest of nature. Read the free Plain Language Summary for this article on the Journal blog.
Published: 2023

22. Analysing the architecture of Corylus avellana and parametrizing L-HAZELNUT FSPM

Author: Grisafi, Francesca, Tombesi, Sergio, Farinelli, Daniela, Boudon, Frédéric, Durand, Jean-Baptiste, Costes, Evelyne, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Università degli Studi di Perugia = University of Perugia (UNIPG), 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, 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), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Modèles statistiques bayésiens et des valeurs extrêmes pour données structurées et de grande dimension (STATIFY), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Dr. Susann Müller, Tsu-Wei Chen, Andreas Fricke, Katrin Kahlen, and Susann Müller and Hartmut Stützel
Subjects: modelling, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], hazelnut, Lpy, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract: International audience; Introduction - Tree architecture is a fundamental part of a functional structural plant model. This is particularly evident in perennial tree crops where the structure of the plant influences the position of source and sink organs, as well as light interception inside the canopy, and serves as storage pool for exceeding carbohydrates. Therefore, a precise description of tree 3D structure is essential to realistically allocate carbohydrates in a FSPM (Costes et al., 2006). Hazelnut tree architecture has different characteristics compared to other fruit tree crops that have been modelled (i.e., peach, mango, apple, and kiwi). It is a monoecious species. Female flowers are grouped into inflorescences located into mixed buds, while male flowers are arranged into inflorescences in the apical position of sylleptic shoots. Each node could bear more than one bud and, the following year, the new shoots are much shorter than the shoots from which they were born. The present study aimed to analyse hazelnut one-year-old shoots 'architecture in order to build the structural part of L-HAZELNUT: a functional structural plant model of hazelnut (Corylus avellana). Material and Methods - Own-rooted tree clones of C.avellana, cultivar “Tonda di Giffoni”, were chosen, during winter, in 2020 and 2021 in Deruta (Italy). Plants were normally irrigated and fertilized. No pruning occurred during the two years. 104 one-year-old proleptic shoots were sampled according to four length categories: short (Sh) when shorter than 5 cm, medium (Me) when they were between 5 and 20 cm, long (Lo) when they were between 20 and 40 cm, and very long (VLo) when longer than 40 cm. For each shoot, diameter, length, and number of nodes were recorded. From the base of the shoot to its tip, the fate of each node was noted. Four fates are distinguished in C.avellana: blind nodes, vegetative buds, sylleptic shoots and mixed buds. In the year subsequent to sampling, the same measurements were repeated on the lateral shoots that were born from the buds. Statistical analyses were done in 2022, using packages from RStudio. First, exploratory analyses were performed to investigate the distribution of the bud types or sylleptic shoots depending on the rank node along the one-year-old proleptic shoots and thus, to address if there were some homogeneous zone (i.e., zones characterized by a stable distribution of the possible bud fates (Guédon et al., 2001)). This led us to draw a flux diagram (Figure 1). Each part of the diagram corresponds to specific logical connections, between FSPM components, which were addressed using specific probabilistic models, inferred from the collected data set. Results and Discussion - During this study new knowledge regarding the architecture of C.avellana was acquired. Even though male flowers were stated to be located on proleptic shoots 'nodes (Botta & Valentini, 2018), we instead highlighted the presence of male flowers in the apical position of sylleptic shoots. It was also observed that hazelnut has a sympodial growth. Each statistical model, associated with the FSPM components, was used to define functions to answer each of the questions addressed in the flow diagram. All the functions were coded in L-py (Boudon et al., 2012) to build a L-system program able to generate the architecture of hazelnut (Figure 1). Conclusion - This led to a first coarse FSPM named L-HAZELNUT, in reference to some previous FSPM for fruit tree crops (Lopez et al., 2010). It simulates the growth of a hazelnut tree over two successive years. The conception of an FSPM is a long and meticulous process that requires having in mind a clear scheme that describes the growing and branching processes. Such a scheme can be acquired by appropriate observations and analyses of how the plant grows and develops. However, as many aspects of the plant have to be considered, the accuracy of the presented 3D structure has still to be evaluated and further studies will be necessary to validate them. Moreover, L-HAZELNUT model should be complemented in the next future with a functional part describing carbon acquisition and partitioning within the tree.
Published: 2023

23. Mapping of QTLs Associated with Biological Nitrogen Fixation Traits in Peanuts (Arachis hypogaea L.) Using an Interspecific Population Derived from the Cross between the Cultivated Species and Its Wild Ancestors

Author: Darius T. Nzepang, Djamel Gully, Joël R. Nguepjop, Arlette Zaiya Zazou, Hodo-Abalo Tossim, Aissatou Sambou, Jean-François Rami, Valerie Hocher, Saliou Fall, Sergio Svistoonoff, Daniel Fonceka, Centre d'Etude Regional Pour l'Amelioration de l'Adaptation A la Secheresse (CERAAS), 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), 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), 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, Institut de Recherche Agricole pour le Développement [Yaoundé] (IRAD), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and German Academic Exchange Service (DAAD), the Avril Foundation, and the Research Allowance for a Southern Thesis (ARTS) for providing a PhD scholarship.
Subjects: sustainable agriculture, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Peanut, wild species, Genetics, peanut, symbiosis, plant nutrition, Genetics (clinical)
Abstract: International audience; Peanuts (Arachis hypogaea L.) are an allotetraploid grain legume mainly cultivated by poor farmers in Africa, in degraded soil and with low input systems. Further understanding nodulation genetic mechanisms could be a relevant option to facilitate the improvement of yield and lift up soil without synthetic fertilizers. We used a subset of 83 chromosome segment substitution lines (CSSLs) derived from the cross between a wild synthetic tetraploid AiAd (Arachis ipaensis × Arachis duranensis) 4× and the cultivated variety Fleur11, and evaluated them for traits related to BNF under shade-house conditions. Three treatments were tested: without nitrogen; with nitrogen; and without nitrogen, but with added0 Bradyrhizobium vignae strain ISRA400. The leaf chlorophyll content and total biomass were used as surrogate traits for BNF. We found significant variations for both traits specially linked to BNF, and four QTLs (quantitative trait loci) were consistently mapped. At all QTLs, the wild alleles decreased the value of the trait, indicating a negative effect on BNF. A detailed characterization of the lines carrying those QTLs in controlled conditions showed that the QTLs affected the nitrogen fixation efficiency, nodule colonization, and development. Our results provide new insights into peanut nodulation mechanisms and could be used to target BNF traits in peanut breeding programs.
Published: 2023

24. An update of evidence for pathogen transmission by ticks of the genus Hyalomma

Author: Sarah I. Bonnet, Stéphane Bertagnoli, Alessandra Falchi, Julie Figoni, Johanna Fite, Thierry Hoch, Elsa Quillery, Sara Moutailler, Alice Raffetin, Magalie René-Martellet, Gwenaël Vourc’h, Laurence Vial, Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), EA Bioscope Corse Méditerranée : Dynamique des infections virales en milieu insulaire, Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Direction de l'Evaluation des Risques (DER), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Hospitalier Intercommunal Villeneuve-Saint-Georges (CHIV), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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: Microbiology (medical), Infectious Diseases, General Immunology and Microbiology, vectorial competence, Immunology and Allergy, tick-borne pathogens, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Molecular Biology, Hyalomma sp, ticks
Abstract: This narrative review was conducted by the ad hoc subgroup from the working expert group on the risks related to Hyalomma ticks at the French Agency for Food, Environmental and Occupational Health & Safety (ANSES) commissioned by the French authorities.; International audience; Current and likely future changes in the geographic distribution of ticks belonging to the genus Hyalomma are of concern, as these ticks are believed to be vectors of many pathogens responsible for human and animal diseases. However, we have observed that for many pathogens there are no vector competence experiments, and that the level of evidence provided by the scientific literature is often not sufficient to validate the transmission of a specific pathogen by a specific Hyalomma species. We therefore carried out a bibliographical study to collate the validation evidence for the transmission of parasitic, viral, or bacterial pathogens by Hyalomma spp. ticks. Our results show that there are very few validated cases of pathogen transmission by Hyalomma tick species.
Published: 2023

25. Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes’ Selective Footprints in the Genes Network Regulating Flowering Time

Author: Nourollah AHMADI, Mamadou Billo BARRY, Julien FROUIN, Miguel de Navascués, Mamadou Aminata Touré, 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, 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), Développement Adaptatif du Riz [AGAP] (DAR), 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 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, Institut de Recherche Agronomique de Guinée (IRAG), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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, and Funding institution: AGROPOLIS Foundation. Grant number: 0900-001-1. Grant recipient: Nourollah Ahmadi.
Subjects: Climate changes, Temporal cline, O. glaberrima, Flowering time, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Soil Science, Rice, Plant Science, Selection footprint, Genome scan, Agronomy and Crop Science, O. sativa
Abstract: Passport and phenotypic data of the rice accessions studied are provided Additional file 11: Table S1. Genotypic data can be downloaded in HapMap format from http://tropgenedb.cirad.fr/tropgene/JSP/interface.jsp?module=RICE study Genotypes, study type G-panel_GBS_data.; International audience; Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops.
Published: 2023

26. Comparative assessment of heat tolerance in weevils associated with a fire‐prone ecosystem

Author: Marion Javal, John S. Terblanche, Chantelle Smit, Julien Haran, Stellenbosch University, Department of Conservation Ecology and Entomology, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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 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), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), The authors thank the Western Cape Nature Conservation Board (Permit No. CN44-30-4229) and the Cape Research Centre, South African National Parks (Permit No. CRC/2019-2020/012-2012/V1) for permission to collect specimens in areas under their control. The authors acknowledge Paula Strauss, Gary Beukman, and Michael Lutzeyer for access to the Grootbos Private Nature Reserve and their friendly assistance during sampling. The authors thank Laurene Dubreuil for introducing Julien Haran and Marion Javal to the Montagu region. Henrika Bosua (Stellenbosch University) is warmly thanked for her help with the respirometry measurements. This study was supported by recurring funding from Montpellier University (Marion Javal) and Cirad (Julien Haran)., and Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE)
Subjects: Coleoptera, Bogert effect, heat knockdown, Ecology, Insect Science, [SDV]Life Sciences [q-bio], fynbos, thermolimit respirometry, insect
Abstract: Data for the HKD experiment is available here: https://doi.org/10.6084/m9.figshare.21647015.; International audience; 1. Fire is an important cause of disturbance which directly shapes many ecosystems worldwide. While the effect of fire on the distribution and regeneration of plant species has been widely documented, little is known on how phytophagous insects are reacting to these disturbances.2. This study explores the survival strategies of various weevil species, a highly diverse phytophagous beetle group in fire-prone ecosystems of the biodiversity hotspot of the Cape Floristic Region in South Africa. More specifically, we investigated how the lifestyle of species (location of larval development, phenology of adults, and flight ability) correlates with heat tolerance. We hypothesized that wingless species in particular will show better tolerance to heat as they have a limited ability to escape fire rapidly and usually remain hidden in the soil.3. The thermal tolerance of a set of sixteen species with divergent lifestyles and geographic distribution was measured using a standard heat knockdown protocol at 48°C. Respirometry was then performed on the most resistant species using a ramping protocol in order to determine CTmax.4. Our results show that the species tested exhibit high variation in thermal tolerance across taxonomic groups, clustering into three modalities: weak, intermediate, and high tolerance to heat stress. In addition, life history traits (diurnal vs. nocturnal adult activity and location of juvenile stages in plant tissues) likely better explain thermal tolerance at the species level than flight ability or the fire-proneness of ecosystems. Finally, results revealed that some non-flying weevil species are highly heat tolerant with CTmax values reaching up to 50.2 and 51.9°C in species among the Ocladiinae and Brachycerinae subfamilies, respectively.5. Climate change is leading to an increase in the impact and frequency of fires. In this context, this study highlights the diversity of strategies developed by arthropods to escape extreme heat in fire prone ecosystems. Further work is necessary to examine the generality of these patterns across other fire prone ecosystems to better understand behavioural compensation and evolutionary responses, especially given the forecast increases in fire driven by drying and warming associated with climate change.
Published: 2023

27. Long-Term Anthropogenic Management and Associated Loss of Plant Diversity Deeply Impact Virome Richness and Composition of Poaceae Communities

Author: François Maclot, Virginie Debue, Carolyn M. Malmstrom, Denis Filloux, Philippe Roumagnac, Mathilde Eck, Lucie Tamisier, Arnaud G. Blouin, Thierry Candresse, Sébastien Massart, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Laboratory of Plant pathology - TERRA - Gembloux Agro-Bio Tech, Liege University, Michigan State University [East Lansing], Michigan State University 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)-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), Agroscope, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fonds de la Recherche Scientifique under grant numbers 1.1.309.19F06 and J.0149.20., and Michigan State University AgBioResearch
Subjects: Microbiology (medical), Infectious Diseases, General Immunology and Microbiology, Ecology, Physiology, [SDV]Life Sciences [q-bio], Genetics, Cell Biology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; Modern agriculture has influenced plant virus emergence through ecosystem simplification, introduction of new host species, and reduction in crop genetic diversity. Therefore, it is crucial to better understand virus distributions across cultivated and uncultivated communities in agro-ecological interfaces, as well as virus exchange among them. Here, we advance fundamental understanding in this area by characterizing the virome of three co-occurring replicated Poaceae community types that represent a gradient of grass species richness and management intensity, from highly managed crop monocultures to little-managed, species-rich grasslands. We performed a large-scale study on 950 wild and cultivated Poaceae over 2 years, combining untargeted virome analysis down to the virus species level with targeted detection of three plant viruses. Deep sequencing revealed (i) a diversified and largely unknown Poaceae virome (at least 51 virus species or taxa), with an abundance of so-called persistent viruses; (ii) an increase of virome richness with grass species richness within the community; (iii) stability of virome richness over time but a large viral intraspecific variability; and (iv) contrasting patterns of virus prevalence, coinfections, and spatial distribution among plant communities and species. Our findings highlight the complex structure of plant virus communities in nature and suggest the influence of anthropogenic management on viral distribution and prevalence.
Published: 2023

28. Current evidences of the efficacy of mosquito mass-trapping interventions to reduce Aedes aegypti and Aedes albopictus populations and Aedes-borne virus transmission

Author: Ali Jaffal, Johanna Fite, Thierry Baldet, Pascal Delaunay, Frédéric Jourdain, Ronald Mora-Castillo, Marie-Marie Olive, David Roiz, Direction de l'Evaluation des Risques (DER), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Centre Hospitalier Universitaire de Nice (CHU Nice), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), WHO Country Office [Kigali, Rwanda] (WHO), and Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)
Subjects: Infectious Diseases, [SDV]Life Sciences [q-bio], Public Health, Environmental and Occupational Health
Abstract: Background Over the past decades, several viral diseases transmitted by Aedes mosquitoes—dengue, chikungunya, Zika—have spread outside of tropical areas. To limit the transmission of these viruses and preserve human health, the use of mosquito traps has been developed as a complement or alternative to other vector control techniques. The objective of this work was to perform a systematic review of the existing scientific literature to assess the efficacy of interventions based on adult mosquito trap to control Aedes population densities and the diseases they transmit worldwide. Methods and findings Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a systematic review was conducted using the PubMed and Scopus databases. Among the 19 selected papers, lethal ovitraps were used in 16 studies, host-seeking female traps in 3 studies. Furthermore, 16 studies focused on the control of Ae. aegypti. Our review showed great heterogeneity in the indicators used to assess trap efficacy: e.g., the number of host-seeking females, the number of gravid females, the proportion of positive containers, the viral infection rate in female mosquitoes or serological studies in residents. Regardless of the type of studied traps, the results of various studies support the efficacy of mass trapping in combination with classical integrated vector control in reducing Aedes density. More studies with standardized methodology, and indicators are urgently needed to provide more accurate estimates of their efficacy. Conclusions This review highlights gaps in the demonstration of the efficacy of mass trapping of mosquitoes in reducing viral transmission and disease. Thus, further large-scale cluster randomized controlled trials conducted in endemic areas and including epidemiological outcomes are needed to establish scientific evidence for the reduction of viral transmission risk by mass trapping targeting gravid and/or host-seeking female mosquitoes.
Published: 2023

29. Rethinking the nature of intraspecific variability and its consequences on species coexistence

Author: Camille Girard-Tercieux, Isabelle Maréchaux, Adam T. Clark, James S. Clark, Benoît Courbaud, Claire Fortunel, Joannès Guillemot, Georges Künstler, Guerric le Maire, Raphaël Pélissier, Nadja Rüger, Ghislain Vieilledent, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Karl-Franzens-Universität Graz, Duke University [Durham], Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), 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), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Français de Pondichéry (IFP), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Universität Leipzig, German Centre for Integrative Biodiversity Research (iDiv), Smithsonian Tropical Research Institute, Département Systèmes Biologiques (Cirad-BIOS), Fondation pour la Recherche sur la Biodiversité, and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: Environmental variation, Individual variation, Competition, Ecology, Intraspecific variability, Species coexistence, Spatial heterogeneity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, High-dimensional niche, Spatial autocorrelation, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract: ContextIntraspecific variability (IV) has been proposed to explain species coexistence in diverse communities. Assuming, sometimes implicitly, that conspecific individuals can perform differently in the same environment and that IV blurs species differences, previous studies have found contrasting results regarding the effect of IV on species coexistence.ObjectiveWe aim at showing that the large IV observed in data does not mean that conspecific individuals are necessarily different in their response to the environment and that the role of high-dimensional environmental variation in determining IV has been largely underestimated in forest plant communities.Methods and ResultsWe first used a simulation experiment where an individual attribute is derived from a high-dimensional model, representing “perfect knowledge” of individual response to the environment, to illustrate how a large observed IV can result from “imperfect knowledge” of the environment. Second, using growth data from clonal Eucalyptus plantations in Brazil, we estimated a major contribution of the environment in determining individual growth. Third, using tree growth data from long-term tropical forest inventories in French Guiana, Panama and India, we showed that tree growth in tropical forests is structured spatially and that despite a large observed IV at the population level, conspecific individuals perform more similarly locally than compared with heterospecific individuals.SynthesisAs the number of environmental dimensions that are typically quantified is generally much lower than the actual number of environmental dimensions influencing individual attributes, a great part of observed IV might be misinterpreted as random variation across individuals when in fact it is environmentally-driven. This mis-representation has important consequences for inference about community dynamics. We emphasize that observed IV does not necessarily impact species coexistence per se but can reveal species response to high-dimensional environment, which is consistent with niche theory and the observation of the many differences between species in nature.
Published: 2023

30. A sex-structured model of Wolbachia invasion to design sex-biased release strategies in Aedes spp mosquitoes populations

Author: Pierre-Alexandre Bliman, Yves Dumont, Oscar Eduardo Escobar-Lasso, Hector J. Martinez-Romero, Olga Vasilieva, Modelling and Analysis for Medical and Biological Applications (MAMBA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), AMAP Lab [Saint-Pierre - La réunion], Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Mathematics and Applied Mathematics [Pretoria], University of Pretoria [South Africa], Universidad del Valle [Cali] (Univalle), E. Escobar, Hector J. Martinez, and Olga Vasilieva acknowledge financial support from the National Fund for Science, Technology, and Innovation (Autonomous Heritage Fund Francisco José de Caldas) by way of the Research Program No. 1106-852-69523, Contract: CT FP 80740-439-2020 (Colombian Ministry of Science, Technology, and Innovation – Minciencias), Grant ID: CI-71241 (Universidad del Valle). The endorsement obtained from the STIC AmSud Program for regional cooperation (20-STIC-05 NEMBICA project) is gratefully recognized by all authors., Yves Dumont is (partially) supported by the DST/NRF SARChI Chair in Mathematical Models and Methods in Biosciences and Bioengineering at the University of Pretoria (Grant 82770). Yves Dumont acknowledges the support of DST/NRF Incentive Grant (Grant 119898) and the support of the Conseil Régional de la Réunion, the Conseil Départemental de la Réunion, the European Agricultural Fund for Rural Development (EAFRD) and the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)., Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), 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), and E. Escobar, Hector J. Martinez, and Olga Vasilieva acknowledge financial support from the National Fund for Science, Technology, and Innovation (Autonomous Heritage Fund Francisco José de Caldas) by way of the Research Program No. 1106-852-69523, Contract: CT FP 80740-439-2020 (Colombian Ministry of Science, Technology, and Innovation – Minciencias), Grant ID: CI-71241 (Universidad del Valle). The endorsement obtained from the STIC AmSud Program for regional cooperation (20-STIC-05 NEMBICA project) is gratefully recognized by all authors. Yves Dumont is (partially) supported by the DST/NRF SARChI Chair in Mathematical Models and Methods in Biosciences and Bioengineering at the University of Pretoria (Grant 82770). Yves Dumont acknowledges the support of DST/NRF Incentive Grant (Grant 119898) and the support of the Conseil Régional de la Réunion, the Conseil Départemental de la Réunion, the European Agricultural Fund for Rural Development (EAFRD) and the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD).
Subjects: Applied Mathematics, biochemical phenomena, metabolism, and nutrition, Aedes spp, Male-biased releases, Population replacement, Modeling and Simulation, parasitic diseases, Numerical simulations, bacteria, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Qualitative Analysis, [MATH]Mathematics [math], Sex-structured model, Wolbachia symbiont, reproductive and urinary physiology, Ordinary differential equations
Abstract: Laboratory experiments as well as some field essays have revealed that the intracellular bacterium Wolbachia, deliberately introduced in Aedes spp female mosquitoes, drastically reduces their vector competence for dengue virus and, also, other mosquito-borne viral diseases. However, female mosquitoes infected with Wolbachia still need to ingest human blood while male mosquitoes, either wild or Wolbachia-carrying, do not bite people. As such, Wolbachia-carrying females may transmit the virus to people during blood-feeding, even though with far less probability than the wild ones. Therefore, massive releases of Wolbachia-carrying females may increase both the nuisance and the epidemiological risk among human residents. With the goal of exploring in depth the practical aspects of sex-biased releases, we introduce in this paper a simple sex-structured model of Wolbachia invasion that brings forward the possibility of developing male-biased release strategies of Wolbachia-carriers leading to Wolbachia invasion. Thanks to this model, we study at length the minimal amount of mosquitoes necessary to complete this task, according to the relative sex-ratio of the released mosquitoes and the release schedule. We also pay attention to the estimate of the time needed to achieve the ultimate population replacement.
Published: 2023

31. Interventions privilégiées en matière d'élevage pour les petits éleveurs dans la zone de conservation transfrontalière du Grand Limpopo : une approche systémique axée sur la demande

Author: Gobvu, Vimbai, Ncube, Sharai, Imbayarwo-Chikosi, Venancio E., Bourgeois, Robin, Mugabe, Prisca, Caron, Alexandre, University of Zimbabwe (UZ), University of Eswatini, Acteurs, Ressources et Territoires dans le Développement (UMR ART-Dev), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Paul-Valéry - Montpellier 3 (UPVM)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Eduardo Mondlane University, and European Project: FED/2017394-443
Subjects: Livestock production, scenario planning, bottom-up approach, Transfrontier Conservation Area, bottomup approach, small-scale farming, participatory approach, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, [SDE.ES]Environmental Sciences/Environmental and Society
Abstract: International audience; In southern Africa, residents of Transfrontier Conservation Areas practice small-scale farming in semi-arid environments constrained by the presence of protected areas and extensive wildlife/livestock/human interfaces that come with conflicts and opportunities. Under these contexts, livestock production aims at supporting local livelihoods despite the harsh semi-arid environment and conflicts with wildlife. In order to promote local development and the well-being of TFCA residents, prioritization of livestock interventions adapted to the local context is needed. The objective of this study was to explore a methodology to list demand-driven interventions for livestock production (cattle, small ruminants and chicken) in a communal land in Zimbabwe. This study used the outputs of an anticipatory scenario-building workshop and individual questionnaires to establish possible and desired livestock interventions by local stakeholders. Results from both the co-elaborative scenario building workshops and the questionnaire survey had participants preferring almost the same interventions that were: restocking herds with breeds adapted to local production; training in livestock practices and production; support to marketing; feed development and value addition; loan schemes to invest in livestock housing and stockfeeds; and finally, animal health interventions to reduce the heavy disease burden. The individual questionnaire data specified preferred interventions for each domestic species. These demand-driven interventions provide a basis for future development projects in the area and avoid top-down approaches by development agencies that fail to address local needs and lack appropriation by local stakeholders necessary for the sustainability of the interventions.; En Afrique australe, les habitants des zones de conservation transfrontalières (TFCA) pratiquent une agriculture à petite échelle dans des environnements semi-arides contrainte par la présence de zones protégées et de vastes interfaces faune/bétail/homme qui s'accompagnent de conflits et d'opportunités. Dans ces contextes, l'élevage vise à soutenir les moyens de subsistance locaux. Afin de promouvoir le bien-être des résidents des TFCAs, il est nécessaire de prioriser des interventions en matière d'élevage adaptées au contexte local. L'objectif de cette étude était d'explorer une méthodologie permettant de dresser une liste d’interventions pour la production animale (bovins, petits ruminants et poulets) dans une zone communale du Zimbabwe. Cette étude s'est appuyée sur les résultats d'un atelier d'élaboration de scénarios et sur des questionnaires individuels pour établir les interventions possibles et souhaitées en matière d'élevage par les parties prenantes locales. Les résultats desateliers de construction de scénarios et de l'enquête par questionnaire ont montré que les mêmes interventions étaient identifiées par les deux approches, à savoir : le repeuplement des troupeaux avec des races adaptées à la production locale ; la formation aux pratiques d'élevage et à la production ; le soutien à la commercialisation ; le développement des aliments pour animaux et la création de valeur ajoutée ; les programmes de prêts financiers pour investir dans les bâtiments d'élevage et les aliments pour animaux ; et enfin, les interventions en matière de santé animale pour réduire la lourde charge de morbidité. Les données du questionnaire individuel ont spécifié les interventions préférées pour chaque espèce domestique. Ces interventions axées sur la demande fournissent une base pour les futurs projets de développement dans la région et évitent des approches descendantes des agences de développement qui ne répondent pas aux besoins locaux et manquent d'appropriation par les parties prenantes locales, nécessaires à la durabilité des interventions.
Published: 2023

32. Improving the nutritional quality of pulses via germination

Author: Luiza Avezum, Eric Rondet, Christian Mestres, Nawel Achir, Yann Madode, Olivier Gibert, Charlotte Lefevre, Youna Hemery, Jean-Luc Verdeil, Loïc Rajjou, 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)-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, Université d’Abomey-Calavi - Faculté des sciences agronomiques (UAC FSA), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), 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, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Labex [AGRO 2011-LABX-002]
Subjects: F60 - Physiologie et biochimie végétale, General Chemical Engineering, Composition des aliments, seeds, Q02 - Traitement et conservation des produits alimentaires, Traitement des aliments, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Légumineuse à grains, Q04 - Composition des produits alimentaires, Semence, Pulses, nutritional compounds, food, food and beverages, Amélioration de qualités nutritives, Valeur nutritive, germination, Plantule, processing, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: International audience; Germination is a traditional process and a re-emerging trend in healthy foods, resulting a progressively increase in scientific research on their nutritional traits and phytochemical contents. This review examines the physiological and biochemical changes during the germination sensu stricto in pulses, taking into consideration the genotype, environmental conditions, hormone control, and the metabolic transition from seed to seedling. Germination sensu stricto is achieved as soon as elongation of the radicle, implies heterotrophy metabolism; further thermal processing is needed before consumption. In contrast, seedlings production requires a long period of imbibition and can provide a ready-to-eat food product. Furthermore, proteins, carbohydrates, minerals, vitamins, and antinutritional compounds of pulses are described. Impacts of food processing, such as soaking, germination, and cooking, in nutritional and antinutritional values are also evaluated. The association of soaking, germination, and cooking increases the nutritional values of pulses by increasing protein/starch digestibility and vitamins content and by decreasing antinutritional compounds. The final plant-based product allows versatility in formulation to produce novel food products and/or ingredients with better nutritional content. This can encourage the scientific community, industry, and government to invest in research and development to increase germinated pulse-based food, to replace other products, or to develop new ones.
Published: 2022

33. Fragmented landscape generator (flsgen): A neutral landscape generator with control of landscape structure and fragmentation indices

Author: Gregoire Blanchard, Xavier Lorca, Dimitri Justeau-Allaire, Philippe Birnbaum, Ghislain Vieilledent, Thomas, Paul Ibanez, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Institut Agronomique Néo-Calédonien (IAC), IMT École nationale supérieure des Mines d'Albi-Carmaux (IMT Mines Albi), Institut Mines-Télécom [Paris] (IMT), Centre Génie Industriel (CGI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: Neutral landscape, Landscape ecology, Application des ordinateurs, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Artificial landscape generation, Programmation informatique, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Constraint programming, Landscape indices, Ecology, Evolution, Behavior and Systematics, Paysage, fragmentation de l'habitat, U10 - Informatique, mathématiques et statistiques, Contrainte, Ecological Modeling, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Habitat fragmentation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Modèle stochastique, Modèle mathématique
Abstract: International audience; 1. Neutral landscape models have many applications in ecology, such as supporting spatially-explicit simulations, developing, and evaluating landscape indices. However, current approaches provide few options to produce large landscapes with controlled composition and fragmentation indices. 2. We introduce flsgen (Fragmented Landscape Generator), a new neutral landscape generator that address this limitation by providing a high level of control over 14 landscape indices. The main novelty of flsgen is the decomposition of landscape generation into two steps: the solving of a constraint satisfaction problem and the generation of a landscape raster with a stochastic algorithm. The latter relies on a continuous environmental gradient that influences the landscape’s spatial configuration. 3. flsgen can generate fine-grained artificial landscapes in small amounts of time, which makes it suited to produce large landscape series systematically. We demonstrate the features of flsgen through three illustrative use cases. 4. flsgen is a practical and efficient tool that expand the current possibilities of neutral landscape models and widen their potential applications. To facilitate its uptake, flsgen is available as free and open-source software through a Java API, a command-line interface, or an R package.
Published: 2022

34. Wild Boars as Reservoir of Highly Virulent Clone of Hybrid Shiga Toxigenic and Enterotoxigenic Escherichia coli Responsible for Edema Disease, France

Author: Alexandre Perrat, Priscilla Branchu, Anouk Decors, Silvia Turci, Marie-Hélène Bayon-Auboyer, Geoffrey Petit, Vladimir Grosbois, Hubert Brugère, Frédéric Auvray, Eric Oswald, LESUR, Hélène, Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Office français de la biodiversité (OFB), LABOCEA Laboratoire [Plouzané, France], Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and This work was supported by the National Research Institute for Agriculture, Food, and Environment’s GISA metaprogram https://colloque.inrae.fr/metaprogramsworkshops_eng/Metaprograms/GISA) and by funding from the Région Occitanie (grant no. ALDOCT-000610) and Ministry of Agriculture awarded to A.P.
Subjects: Microbiology (medical), Swine, Epidemiology, [SDV]Life Sciences [q-bio], Sus scrofa, Infectious and parasitic diseases, RC109-216, fluids and secretions, Escherichia coli, Stx2e, Animals, Edema, Enterotoxigenic Escherichia coli, Wild Boars as Reservoir of Highly Virulent Clone of Hybrid Shiga Toxigenic and Enterotoxigenic Escherichia coli Responsible for Edema Disease, France, antimicrobial resistance, bacteria, Escherichia coli Infections, F18, Shiga-Toxigenic Escherichia coli, ETEC, Research, pigs, edema disease, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, Clone Cells, [SDV] Life Sciences [q-bio], STEC, Infectious Diseases, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, EDEC, O139:H1, Sus domesticus, Medicine, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, enterotoxin, wild boar
Abstract: International audience; Edema disease is an often fatal enterotoxemia caused by specific strains of Shiga toxin-producing Escherichia coli (STEC) that affect primarily healthy, rapidly growing nursery pigs. Recently, outbreaks of edema disease have also emerged in France in wild boars. Analysis of STEC strains isolated from wild boars during 2013-2019 showed that they belonged to the serotype O139:H1 and were positive for both Stx2e and F18 fimbriae. However, in contrast to classical STEC O139:H1 strains circulating in pigs, they also possessed enterotoxin genes sta1 and stb, typical of enterotoxigenic E. coli. In addition, the strains contained a unique accessory genome composition and did not harbor antimicrobial-resistance genes, in contrast to domestic pig isolates. These data thus reveal that the emergence of edema disease in wild boars was caused by atypical hybrid of STEC and enterotoxigenic E. coli O139:H1, which so far has been restricted to the wildlife environment.Keywords
Published: 2022

35. Synergy between an emerging monopartite begomovirus and a DNA-B component

Author: Ouattara, Alassane, Tiendrébéogo, Fidèle, Becker, Nathalie, Urbino, Cica, Thébaud, Gaël, Hoareau, Murielle, Allibert, Agathe, Chiroleu, Frédéric, Vernerey, Marie-Stéphanie, Traoré, Edgar, Barro, Nicolas, Traoré, Oumar, Lefeuvre, Pierre, Lett, Jean-Michel, Institut de l'Environnement et Recherches Agricoles [Ouagadougou] (INERA), Centre national de la recherche scientifique et technologique [Ouagadougou] (CNRST), 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), Université Joseph Ki-Zerbo [Ouagadougou] (UJZK), LMI Patho-Bios, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), This article was funded by European Union (ERDF) (Grant no. GURDT I2016-1731-0006632), and Agropolis Fondation (Grant no. E-SPACE project number 1504-004).
Subjects: Virulence, Ecology, Evolution, Science, food and beverages, Plants, Microbiology, Article, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Hemiptera, Begomovirus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA, Viral, Animals, Medicine, H20 - Maladies des plantes, Plant Diseases
Abstract: International audience; In recent decades, a legion of monopartite begomoviruses transmitted by the whitefly Bemisia tabaci has emerged as serious threats to vegetable crops in Africa. Recent studies in Burkina Faso (West Africa) reported the predominance of pepper yellow vein Mali virus (PepYVMLV) and its frequent association with a previously unknown DNA-B component. To understand the role of this DNA-B component in the emergence of PepYVMLV, we assessed biological traits related to virulence, virus accumulation, location in the tissue and transmission. We demonstrate that the DNA-B component is not required for systemic movement and symptom development of PepYVMLV (non-strict association), but that its association produces more severe symptoms including growth arrest and plant death. The increased virulence is associated with a higher viral DNA accumulation in plant tissues, an increase in the number of contaminated nuclei of the phloem parenchyma and in the transmission rate by B. tabaci. Our results suggest that the association of a DNA-B component with the otherwise monopartite PepYVMLV is a key factor of its emergence.
Published: 2022

36. AgroLD: a Knowledge Graph for the Plant Sciences

Author: Larmande, Pierre, Pitollat, Bertrand, Tando, Ndomassi, Pomie, Yann, Happi, Bill, Guignon, Valentin, Ruiz, Manuel, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), WEB Architecture x Semantic WEB x WEB of Data (WEB3), 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), 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, 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), The Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT) [Hanoi], Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and ANR-22-CE23-0012,DIG-AI,Decouverte des interactions genotype-phenotype à l'aide de graphe de connaissance et d'IA(2022)
Subjects: FAIR data, Knowledge Graph, Bioinformatics, Linked Data, Plant Sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract: Démonstration; International audience; Recent advances in high-throughput technologies have revolutionized the analysis in the field of the plant sciences. However, there is an urgent need to effectively integrate and assimilate complementary information to understand the biological system in its entirety. We have developed AgroLD, a knowledge graph that exploits Semantic Web technologies to integrate data of interest for the plant science community e.g., rice, wheat, arabidopsis and in this way facilitate the formulation and validation of new scientific hypotheses. AgroLD contains around 900M triples created by annotating and integrating more than 100 datasets coming from 15 data sources. Our objective is to offer a domain specific knowledge platform to answer complex biological and plant sciences questions related to the implication of genes in, for instance, plant disease resistance or adaptative responses to climate change. In this demo, we present some results which currently focused on genomics, genetics and trait associations.
Published: 2023

37. Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense

Author: Moana Peylhard, David Berthier, Guiguigbaza-Kossigan Dayo, Isabelle Chantal, Souleymane Sylla, Sabine Nidelet, Emeric Dubois, Guillaume Martin, Guilhem Sempéré, Laurence Flori, Sophie Thévenon, Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre international de recherche-développement sur l'élevage en zone sub-humide (CIRDES), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 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, 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), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), 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), ANR-11-JSV6-0001,AATTOL,Caractérisation des bases moléculaires de la tolérance à la Trypanosomose Animale Africaine: analyse conjointe des transcriptomes de l'hôte bovin et du parasite(2011), ANR-11-LABX-0024,ParaFrap,Alliance française contre les maladies parasitaires(2011), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: Trypanosoma congolense, [SDV]Life Sciences [q-bio]
Abstract: Animal African trypanosomosis, caused by blood protozoan parasites transmitted mainly by tsetse flies, represents a major constraint for millions of cattle in sub-Saharan Africa. Exposed cattle include trypanosusceptible indicine breeds, severely affected by the disease, and West African taurine breeds called trypanotolerant owing to their ability to control parasite development, survive and grow in enzootic areas. Until now the genetic basis of trypanotolerance remains unclear. Here, to improve knowledge of the biological processes involved in trypanotolerance versus trypanosusceptibility, we identified bovine genes differentially expressed in five West African cattle breeds during an experimental infection byTrypanosoma congolenseand their biological functions. To this end, whole blood genome-wide transcriptome of three trypanotolerant taurine breeds (N’Dama, Lagune and Baoulé), one susceptible zebu (Zebu Fulani) and one African taurine x zebu admixed breed (Borgou) were profiled by RNA sequencing at four time points, one before and three during infection. As expected, infection had a major impact on cattle blood transcriptome regardless of the breed. The functional analysis of differentially expressed genes over time in each breed confirmed an early activation of the innate immune response, followed by an activation of the humoral response and an inhibition of T cell functions at the chronic stage of infection. More importantly, we highlighted overlooked features, such as a strong disturbance in host metabolism and cellular energy production that differentiates trypanotolerant and trypanosusceptible breeds. N’Dama breed showed the earliest regulation of immune response, associated with a strong activation of cellular energy production, also observed in Lagune, and to a lesser extent in Baoulé. Susceptible Zebu Fulani breed differed from other breeds by the strongest modification in lipid metabolism regulation. Overall, this study provides a better understanding of the biological mechanisms at work during infection, especially concerning the interplay between immunity and metabolism that seems differentially regulated depending on the cattle breeds.
Published: 2023

38. Watermelons in the Desert in Morocco: Struggles Around a Groundwater Commons-in-the-Making

Author: Bossenbroek, Lisa, Ftouhi, Hind, Kadiri, Zakaria, Kuper, Marcel, University of Koblenz-Landau, Centre de Recherches et d’Études sur les Sociétés Contemporaines (CRESC), University Hassan II [Casablanca], Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and ANR-18-NT2S-0002,T2GS,Transformations pour une durabilité des eaux souterraines : apprentissages communs des interactions homme-eau(2018)
Subjects: pastèque, Participation communautaire, [SDE.ES]Environmental Sciences/Environmental and Society, U70 - Sciences humaines et sociales, eau souterraine, Morocco, Conservation de l'eau, Arid regions, Commoning, Social practices, approches communautaires, P10 - Ressources en eau et leur gestion, Collective action, Irrigation, Groundwater, Citrullus lanatus, Drâa Valley
Abstract: International audience; Groundwater is essential for early-season agriculture in many arid regions. In such regions, however, groundwater recharge is generally low, leading to groundwater degradation. State responses are seldom effective in addressing this issue, which leads to fatalist narratives of the unsustainability of profitable agricultural growth and the collapse of aquifers. We argue that such narratives make it difficult to recognise more promising instances in which communities find solutions to groundwater degradation. We call for a fine-grained analysis of the social practices around the use of groundwater, which, we argue, represent a process of commoning. We do so while recognising that the collective action of communities is embedded in an intricate set of relations with other stakeholders including the state, and that the positive environmental and transformative social change that is often associated with commoning cannot be taken for granted at the outset. Building on the case of the arid Drâa Valley in Morocco where watermelon production has expanded rapidly, we illustrate how the process of commoning evolves through different social practices, including: 1) the use of new farming practices that reveal the potential of the aquifer; 2) the representation of the aquifer as severely degraded and the development of a narrative around it being a collective good to be protected against outsiders; 3) the defining and negotiating of rules to control groundwater access and use; and 4) the engagement in negotiations and the resolving of conflicts. Our analysis shows that commoning, as performed by young local farmers, is about extending the lifespan of the aquifer for agricultural production rather than preserving it indefinitely; however, an examination of commoning practices also reveals the capacity of the community to change the course of the future.
Published: 2023

39. First Report of African Eggplant Yellowing Virus on Tomato Exhibiting Necrotic Yellowing Symptoms in Northern Côte d’Ivoire

Author: A.-J. N’cho, K. Séka, L. Bele, H. Diallo, T. Martin, N. Coulibaly, L. Fondio, M. Hoareau, P. Lefeuvre, J.-M. Lett, Université Nangui Abrogoua (UNA), Université Félix Houphouët-Boigny (UFHB), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre National de la Recherche Agronomique - CNRA (IVORY COAST), 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), Funding was provided by the European Commission (grant/award no. ERDF - GURDT 12016-1731-0006632)., and European Project: ERDF
Subjects: vegetables, disease management, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, epidemiology, Plant Science, viruses and viroids, Agronomy and Crop Science, pathogen detection, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; In February 2019, virus-like symptoms of necrotic yellowing were observed on tomato plants in a field plot in the locality of Odiénné in the Denguélé region of the north of Côte d’Ivoire (8°14.157′N; 6°26.772′W), together with high disease incidence and dense whitefly populations. The observed symptoms were similar to those associated with the poleroviruses (family Solemoviridae) recently described on pepper (Capsicum spp.) in Benin and on African eggplant (Solanum aethiopicum) in Mali (Afouda et al. 2017). To identity the potential agent(s) causing these symptoms, five samples from symptomatic plants and five samples from asymptomatic plants were collected, dehydrated, and subjected to total RNA extraction using the RNeasy Plant Extraction kit (Qiagen, Courtaboeuf, France). The presence of poleroviruses in the samples was tested by RT-PCR using the universal primers PoconF and PococpR (1.4-kb fragment) designed by Xiang et al. (2008) and modified by Knierim et al. (2010) for the detection of poleroviruses. Two symptomatic samples (CI370 and CI371) tested positive. The RT-PCR product amplified from sample CI371 was directly sequenced in a single direction. BLASTn analysis showed that its nucleotide sequence shared 83.2% identity with that of an isolate of African eggplant yellowing virus from Benin (AeYV; KX856975). Based on this reference sequence, specific primers AeYV-F3249 (5′-GTCTAGGTTTCAAAGTCGAGG-3′) and AeYV-RD4339 (5′-CTACCTATTTKGGRTTGTGCAG-3′) were designed for the amplification of a 1,091-bp product covering part of AeYV ORFs 2 and 3 and used in RT-PCR experiments on total RNA extracted from the 10 tomato leaf samples collected in Odiénné. Amplicons of the expected size were obtained from three symptomatic samples (CI367, CI370, and CI371) and subjected to direct sequencing in both directions. BLASTn analysis showed that all three assembled nucleotide sequences (GenBank accession nos. ON228068, ON228069, and ON228070) were identical and shared 98.4 and 93.7% similarity with sequences of the Beninese (KX856975) and Malian (KX856972) isolates of AeYV, respectively. To our knowledge, this is the first report of AeYV both on tomato and in Côte d’Ivoire. The detection of AeYV on pepper, eggplant, and tomato in several West African countries raises the question of whether this virus is emerging elsewhere in West Africa and on other solanaceous crops. Furthermore, while the majority of poleroviruses are transmitted by aphids (Dombrowsky et al. 2010), recent studies have characterized new whitefly-transmitted poleroviruses in Israel (Ghosh et al. 2019) and Brazil (Costa et al. 2020). The high density of whiteflies observed on diseased plants in Côte d’Ivoire raises the question of whether whiteflies also are a vector of AeYV. The distribution, incidence, transmission, and impacts of AeYV on vegetables in West Africa is still unknown and needs to be further investigated to develop accurate control strategies.
Published: 2023

40. Genetic diversity and molecular epidemiology of Middle East Respiratory Syndrome Coronavirus in dromedaries in Ethiopia, 2017–2020

Author: Ziqi Zhou, Abraham Ali, Elias Walelign, Getnet F. Demissie, Ihab El Masry, Takele Abayneh, Belayneh Getachew, Pavithra Krishnan, Daisy Y.M. Ng, Emma Gardner, Yilma Makonnen, Eve Miguel, Véronique Chevalier, Daniel K. Chu, Ray T. Y. So, Sophie Von Dobschuetz, Gezahegne Mamo, Leo L. M. Poon, Malik Peiris, City University of Hong Kong [Hong Kong] (CUHK), Ethiopian Public Health Institute (EPHI), Addis Ababa University (AAU), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), Haramaya University (HU), National Veterinary Institute [Debre Zeit, Ethiopia] (NVI), The University of Hong Kong (HKU), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), and UK Health Security Agency [London] (UKHSA)
Subjects: Epidemiology, [SDV]Life Sciences [q-bio], Immunology, genetic instability, General Medicine, molecular epidemiology, Microbiology, MERS-CoV, Infectious Diseases, Virology, evolution, Drug Discovery, Parasitology, Ethiopia
Abstract: International audience; Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels and causes zoonotic infection and disease in humans. Although over 80% of the global population of infected dromedary camels are found in Africa, zoonotic disease had only been reported in the Arabia Peninsula and travel-associated disease has been reported elsewhere. In this study, genetic diversity and molecular epidemiology of MERS-CoV in dromedary camels in Ethiopia were investigated during 2017–2020. Of 1766 nasal swab samples collected, 61 (3.5%) were detected positive for MERS-CoV RNA. Of 484 turbinate swab samples collected, 10 (2.1%) were detected positive for MERS-CoV RNA. Twenty-five whole genome sequences were obtained from these MERS-CoV positive samples. Phylogenetically, these Ethiopian camel-originated MERS-CoV belonged to clade C2, clustering with other East African camel strains. Virus sequences from camel herds clustered geographically while in an abattoir, two distinct phylogenetic clusters of MERS-CoVs were observed in two sequential sampling collections, which indicates the greater genetic diversity of MERS-CoV in abattoirs. In contrast to clade A and B viruses from the Arabian Peninsula, clade C camel-originated MERS-CoV from Ethiopia had various nucleotide insertions and deletions in non-structural gene nsp3, accessory genes ORF3 and ORF5 and structural gene N. This study demonstrates the genetic instability of MERS-CoV in dromedaries in East Africa, which indicates that the virus is still actively adapting to its camel host. The impact of the observed nucleotide insertions and deletions on virus evolution, viral fitness, and zoonotic potential deserves further study.
Published: 2023

41. Complete genome sequencing of three clade-1 xanthomonads reveals genetic determinants for a lateral flagellin and the biosynthesis of coronatine-like molecules in Xanthomonas

Author: Chloé Peduzzi, Angeliki Sagia, Daiva Burokiene, Ildikó K. Nagy, Marion Fischer-Le Saux, Perrine Portier, Alexis Dereeper, Sebastien Cunnac, Veronica Roman-Reyna, Jonathan Jacobs, Claude Bragard, Ralf Koebnik, Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Crete [Heraklion] (UOC), Nature Research Centre [Vilnius], Enviroinvest Corp, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), IRHS - Équipe EmerSys (Emergence, Systématique et Ecologie des Bactéries associées aux Plantes) (IRHS-EMERSYS), 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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Ohio State University [Columbus] (OSU), Earth and Life Institute, Applied Microbiology - Phytopathology, 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, 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)-Université de Montpellier (UM)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Evolution, Sequencing, Microbe-genome, Genomics, Plant Science, Agronomy and Crop Science, Bacterial Pathogens, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; Evolutionarily early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, and Xanthomonas translucens, which infects small-grain cereals, diverse grasses, but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches indicated that this clade likely contains more, yet undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. In addition, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
Published: 2023

42. Domestication provides durum wheat with protection from locust herbivory

Author: Marie‐Pierre Chapuis, Nicolas Leménager, Cyril Piou, Pierre Roumet, Héloïse Marche, Julia Centanni, Christophe Estienne, Martin Ecarnot, François Vasseur, Cyrille Violle, Elena Kazakou, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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, 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), 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, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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 Agro Montpellier, This work was supported by the DINER project, publicly funded by the Labex CEMEB and funds from the French Agricultural Research Centre for International Development (CIRAD). CV was supported by the European Research Council (ERC) Starting Grant Project StG-2014-639706-CONSTRAINTS. We thank the CEFE (Centre d'Ecologie Fonctionnelle et Evolutive) and the CBGP (Centre de Biologie pour la Gestion des Populations) for providing us access to the LabEx CeMEB plateform 'terrain d'expérience CEFE,' 43°38′20.2′′N 3°51′51.0′′E, and the SEPA plateform, respectively., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: Ecology, leaf, nutritional ecology, plant toughness, [SDV]Life Sciences [q-bio], domestication syndrome, Locusta migratoria, functional ecology, Triticum turgidum, cereal crop, pest insects, plant nitrogen content, feeding selection, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract: International audience; Lower plant resistance to herbivores following domestication has been suggested as the main cause for higher feeding damage in crops than in wild progenitors. While herbivore compensatory feeding has also been proposed as a possible mechanism for raised damage in crops with low nutritional quality, predictions regarding the effects of plant domestication on nutritional quality for herbivores remain unclear. In particular, data on primary metabolites, even major macronutrients, measured in the organs consumed by herbivores, are scarce. In this study, we used a collection of 10 accessions of wild ancestors and 10 accessions of modern progenies of Triticum turgidum to examine whether feeding damage and selectivity by nymphs of Locusta migratoria primarily depended on five leaf traits related to structural resistance or nutrient profiles. Our results unexpectedly showed that locusts favored wild ancestors over domesticated accessions and that leaf toughness and nitrogen and soluble protein contents increased with the domestication process. Furthermore, the quantitative relationship between soluble protein and digestible carbohydrates was found to poorly meet the specific requirements of the herbivore, in all wheat accessions, both wild and modern. The increase in leaf structural resistance to herbivores in domesticated tetraploid wheat accessions suggested that resource allocation trade-offs between growth and herbivory resistance may have been disrupted by domestication in the vegetative organs of this species. Since domestication did not result in a loss of nutritional quality in the leaves of the tetraploid wheat, our results rather provides evidence for a role of the content of plants in nonnutritive nitrogenous secondary compounds, possibly deterrent or toxic, at least for grasshopper herbivores.
Published: 2023

43. Protéger les cultures en augmentant la diversité végétale des espaces agricoles.: Rapport scientifique de l’Expertise scientifique collective

Author: Vialatte, A., Martinet, Vincent, Tibi, Anaïs, Alignier, Audrey, Angeon, Valérie, Bedoussac, Laurent, Bohan, David, Bougherara, Douadia, Carpentier, A., Castagneyrol, Bastien, Cordeau, Stéphane, Courtois, Pierre, Deguine, Jean-Philippe, Doelher, Marianne, Enjalbert, Jérôme, Fabre, Frédéric, Femenia, Fabienne, Fréville, Hélène, Goulet, Frederic, Grateau, Regis, Grimonprez, Benoît, Gross, Nicolas, Hannachi, Mourad, Jeanneret, Philippe, Labarthe, Pierre, Launay, Marie, Lelievre, Virginie, Lemarié, Stéphane, Martel, Gilles, Masson, Abel, Navarrete, Mireille, Plantegenest, Manuel, Ravigné, Virginie, Rusch, Adrien, Suffert, Frédéric, Tapsoba, Abdoulaye, Thoyer, Sophie, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Paris-Saclay Applied Economics (UMR PSAE), AgroParisTech-Université Paris-Saclay-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), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), AGroécologie, Innovations, teRritoires (AGIR), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Centre d'Economie de l'Environnement - Montpellier (CEE-M), Centre National de la Recherche Scientifique (CNRS)-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), Structures et Marché Agricoles, Ressources et Territoires (SMART), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), 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 (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, Agroclim (AGROCLIM), 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), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Office Français de la Biodiversité (Plan Ecophyto II+), and INRAE
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SHS]Humanities and Social Sciences
Published: 2023

44. Cytogenotoxicity screening of urban and rural marshes: An integrated in vivo approach coupling fish and plant‐based tests adapted for low income countries

Author: Elodie Pepey, Geneviève Conéjéro, Elia Njara Ndrianaivo, Jean‐Luc Verdeil, Jean‐Michel Mortillaro, David Boggio, Modestine Raliniaina, Simon Pouil, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Plateforme d'histocytologie et d'imagerie cellulaire végétale (PHIV), 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, 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 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, 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)-Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-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)-Centre National de la Recherche Scientifique (CNRS)-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)-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 National de Recherche Appliquée au Développement Rural (FOFIFA), Environmental Sciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, and ANR-10-INBS-04
Subjects: Nucleolar alterations, Allium cepa, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Madagascar, Oreochromis niloticus, Environmental Chemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Mitotic index, Comet assay
Abstract: International audience; Effects of anthropogenic activities such as urbanisation, population growth and agriculture on water quality are major concerns particularly in low-income countries where water quality monitoring can be challenging. The purpose of this study was to evaluate the cytogenotoxic potential of water from urban and rural Malagasy marshes, coupling a fish (Nile tilapia Oreochromis niloticus) and a plant (Allium cepa) species as bioindicators. The fish and plants were exposed for 72 h to water sampled in the two locations investigated. DNA strand breaks were assessed using the comet assay on fish erythrocytes, while mitotic index and nucleolar alterations were estimated in cells of the plant root apex. Comet assays revealed significant DNA strand breaks to fish erythrocytes in both the marshes investigated while the mitotic index and nucleolar characteristics in the roots of A. cepa mainly highlighted potential cytotoxicity in the urban marsh. Our results demonstrate the advantages of coupling in vivo biological test systems to screen potential cytogenotoxicity of surface water in low-income countries where comprehensive datasets of aquatic contaminants are often lacking. This article is protected by copyright. All rights reserved. Environ Toxicol Chem 2023;00:0-0. (c) 2023 SETAC.
Published: 2023

45. Suspicions of two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France

Author: Enora Dupas, Karine Durand, Adrien Rieux, Martial Briand, Olivier Pruvost, Amandine Cunty, Nicolas Denancé, Cécile Donnadieu, Bruno Legendre, Céline Lopez-Roques, Sophie Cesbron, Virginie Ravigné, Marie-Agnès Jacques, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), 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), Laboratoire de santé des végétaux (LSV Angers), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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)-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), the GET-PACBIO program (« Programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 ») European Union (European Regional Development Fund, ERDF contract GURDT 2016-1731-0006632), Conseil Régional de La Réunion and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD). Agence Nationale pour la Recherche., and ANR-17-CE35-0009,MUSEOBACT,'Une nuit au musée': mieux reconstuire les emergences de bactéries pathogènes des cultures grâce à des échantillons historiques(2017)
Subjects: MESH: France, MESH: Xylella, Medicine (miscellaneous), MESH: Italy, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Europe, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology
Abstract: Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 × 10-7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Côte d’Azur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations.
Published: 2023

46. Evolution, systematics and historical biogeography of Palparini and Palparidiini antlions (Neuroptera: Myrmeleontidae): Old origin and in situ diversification in Southern Africa

Author: Noémie M.‐C. Hévin, Gael. J. Kergoat, Anne‐Laure Clamens, Bruno Le Ru, Mervyn W. Mansell, Bruno Michel, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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, 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 de Poitiers, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), International Centre of Insect Physiology and Ecology (ICIPE), ICIPE, Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa], Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Financial support was provided by CIRAD (for B. Michel), INRAE (for G.J. Kergoat), by IRD and ICIPE (for B. Le Ru). Some of the sequencing was also supported by the programme BdV (Project ICONE) supported by a joint CNRS, INRAE, and MNHN consortium and through a collaboration with F.L. Condamine (CNRS, UMR ISEM) as part of another research project.
Subjects: paleoendemism, historical biogeography, Insect Science, Southern Africa, systematics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Afrotropics, Ecology, Evolution, Behavior and Systematics, antlions, out of Africa
Abstract: Newly generated sequences were deposited in GenBank, and are registered with the following accession numbers: OQ581997–OQ582070(cob), OQ603605–OQ603608(18S), OQ606012–OQ606168(cox1), OQ624960–OQ625111(rrnL), OQ625113–OQ625252(rrnS) and OQ625254–OQ625279(28S) (see Table S2 for details).This study is dedicated to Dr. André Prost, who passed away on February 3, 2023. André Prost was a well-recognized Neuroptera specialist (former secretary of the International Association of Neuropterology), with a special interest for the West African fauna.Merwyn W.Mansell gratefully acknowledges the following organizations and people who contributed to research on antlion diversity in SouthernAfrica: Oppenheimer Generations Research and Conservation, the Tswalu Foundation, and Nicky, Jonathan and Strilli Oppenheimer ,who have actively encouraged and permitted Neuroptera research in their private reserves, Tswalu Kalahari Reserve and Rooipoort; Duncan MacFadyen (Oppenheimer Generations, Head Research and Con-servation), Dylan Smith (Tswalu Kalahari Reserve), who facilitated ourvisits and provided key specimens. Also, (i) the National Parks Boardof South Africa is acknowledged for permits enabling Neuroptera research in the Kalahari Gemsbok National Park (now Kgalagadi Transfrontier Park), the Kruger National Park and Karoo National Park,and the staff of these parks who enabled the visits and provided valuable material: (L.E.O. Braack, A. Braack, H. Braack; Dr S. Joubert), (C.E.O., Kruger Park); (ii) Northern Cape Nature Conservation is thanked for providing permits for the northern Cape region; (iii) the KwaZulu-Natal Parks are acknowledged for permission to work on their reserves. Dr M.K. Seely, Director of the Namib Desert Research Station at Gobabeb is thanked for providing facilities and much scientifico-operation over the years; (iv) the Directorate of Nature Conservation and Recreational Resorts of Namibia are acknowledged for use offacilities at Gobabeb and permission to work in the Namib/NaukluftPark, many years ago. Professor Clarke H. Scholtz (University of Pretoria) is especially thanked for organizing many of the field trips thatprocured important material. Merwyn W. Mansell also gratefullyacknowledges the following people especially, for providing crucial specimens: J.B. Ball (University of Pretoria), A.K. (Tony) Brinkman, A.J.Gardiner, H. de Klerk, P. Hawkes, D.M. Kroon, W. Jubber, A.P. Marais,R.W. Mansell, L.R. Minter, R.G. Oberprieler, H.S Staude, R.D. Stephenand those mentioned in Mansell and Oswald (2023). The JRS Biodiversity Foundation and GBIF are sincerely thanked for funding M.W.Mansell’s Southern African Lacewing project, especially the development of the “Palpares Relational Database” designed by Brian Kenyon,which underpinned the accumulation and collation of much data usedin this presentation, for which he is gratefully acknowledged. Whileworking at icipe (African Insect Science for Food and Health), B. Le Rubenefited from research and collect permits delivered by the KenyaPlant Health Inspectorate Service (KEPHIS) (B. Le Ru thanks A. Kibe,B. Musyoka, L. Ngala, G. Okuku and G. Ong’amo) and the Plant Pro-tection Division of the Ministry of Agriculture of Botswana (B. Le Ru EVOLUTION AND SYSTEMATICS OF PALPARINE ANTLIONS thanks C. Nyakumondiwa, R. Mutamisha and E. Moeng). Bruno Michel also thanks the following people for providing several interesting specimens: B.F. Jacobs (Southern Methodist University, USA), M.Martinez (INRAE) and J.-Y. Rasplus (INRAE). We gratefully acknowledge the late A. Prost for communicating important information on the genusNosa. We are also indebted to the following persons whogave us permission to use pictures they took: S. Akame, T. Cardenos,H. de Klerk, G. Kunz, D. Robertson, H. Robertson, H. Roland, W.Roland and A.T. Schoeman. Laboratory facilities were provided by CBGP in France. We are grateful to the Genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing help and/or computing and/or storage resources.; International audience; Palparine and palparidiine antlions constitute an emblematic clade of large and occasionally colourful insects that are only distributed in the western portion of the Eastern hemisphere, with about half of the known species diversity occurring exclusively in Southern Africa. Little is known about their evolutionary history, and the boundaries and relationships of most genera are still unresolved. In this study, we analyse a molecular dataset consisting of seven loci (five mitochondrial and two nuclear genes) for 144 antlion species and provide the first phylogenetic hypothesis for a representative sampling of Palparini and Palparidiini (62 Palparini species, representing 15 of the 17 known genera, and all three known Palparidiini species). In addition, we reconstruct their timing of diversification and historical biogeography. The resulting tree indicates that several extant palparine genera are polyphyletic or paraphyletic and provides interesting leads that ought to be helpful for future taxonomic revisions; it also enables us to re-evaluate the taxonomic utility and relevancy of a number of morphological characters that were previously used to define some genera. Molecular dating analyses indicate that the most recent common ancestor of both groups originated about 92 million years ago (Ma) in the Late Cretaceous. Finally, the results of historical biogeography analyses provide strong support for an origin in Southern Africa, which further acted as both a cradle of diversification and a springboard for successive waves of northern dispersals.
Published: 2023

47. Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea

Author: Guillaume Martin, Aurélien Cottin, Franc‐Christophe Baurens, Karine Labadie, Catherine Hervouet, Frédéric Salmon, Nilda Paulo‐de‐la‐Reberdiere, Ines Van den Houwe, Julie Sardos, Jean‐Marc Aury, Angélique D'Hont, Nabila Yahiaoui, 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, 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), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: Introgression, [SDV]Life Sciences [q-bio], Plant Science, F30 - Génétique et amélioration des plantes, domestication, Variation génétique, F01 - Culture des plantes, Genetics, hybridization, Musa spp, Diversité génétique (comme ressource), Domestication des plantes, phytogénétique, Musa, Cell Biology, genetic diversity, Hybridation interspécifique, genome ancestry
Abstract: International audience; Hybridizations between Musa species and subspecies, enabled by their transport via human migration, were proposed to have played an important role in banana domestication. We exploited sequencing data of 226 Musaceae accessions, including wild and cultivated accessions, to characterize the inter(sub)specific hybridization pattern that gave rise to cultivated bananas. We identified 11 genetic pools that contributed to cultivars, including two contributors of unknown origin. Informative alleles for each of these genetic pools were pinpointed and used to obtain genome ancestry mosaics of accessions. Diploid and triploid cultivars had genome mosaics involving three up to possibly seven contributors. The simplest mosaics were found for some diploid cultivars from New Guinea, combining three contributors, i.e., banksii and zebrina representing Musa acuminata subspecies and, more unexpectedly, the New Guinean species Musa schizocarpa. Breakpoints of M. schizocarpa introgressions were found to be conserved between New Guinea cultivars and the other analyzed diploid and triploid cultivars. This suggests that plants bearing these M. schizocarpa introgressions were transported from New Guinea and gave rise to currently cultivated bananas. Many cultivars showed contrasted mosaics with predominant ancestry from their geographical origin across Southeast Asia to New Guinea. This revealed that further diversification occurred in different Southeast Asian regions through hybridization with other Musa (sub)species, including two unknown ancestors that we propose to be M. acuminata ssp. halabanensis and a yet to be characterized M. acuminata subspecies. These results highlighted a dynamic crop formation process that was initiated in New Guinea, with subsequent diversification throughout Southeast Asia.
Published: 2023

48. The potential of Rhipicephalus microplus as a vector of Ehrlichia ruminantium in West Africa

Author: Mireille V. Some, Abel S. Biguezoton, Naftaly Githaka, Hassane Adakal, Guiguigbaza-Kossigan Dayo, Adrien Belem, Sébastien Zoungrana, Frédéric Stachurski, Christine Chevillon, Centre international de recherche-développement sur l'élevage en zone sub-humide (CIRDES), Institut du Développement Rural, Université Polytechnique Nazi Boni Bobo-Dioulasso (UNB), International Livestock Research Institute [CGIAR, Nairobi] (ILRI), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Université Dan Dicko Dan koulodo de Maradi (UDDM), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), and This work benefited from two grants: an International Foundation of Science (IFS) grant to Abel BIGUEZOTON ( I-1-B-5224-2 ) and a student grant from the International Mixed Laboratory on Vector-borne Diseases (LAMIVECT 2) to Mireille SOME.
Subjects: Vertical vs horizontal transmission, heartwater [EN], Rickettsiose, L73 - Maladies des animaux, Microbiology, Heartwater, West Africa, Ehrlichia ruminantium, Transmission des maladies, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Santé animale, Amblyomma variegatum, Épidémiologie, Infectious Diseases, Vecteur de maladie, Rhipicephalus microplus, Insect Science, Parasitology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Vector competence, L72 - Organismes nuisibles des animaux
Abstract: International audience; Heartwater, or cowdriosis, is a virulent tick-borne rickettsial disease of ruminants caused by Ehrlichia ruminantium, biologically transmitted by Amblyomma species (A. variegatum in West Africa). In West Africa, this bacterium was recently reported to naturally infect the invasive cattle tick, Rhipicephalus microplus (Rm) through trans-ovarian transmission from replete adult females to offspring. A ‘sheep-tick-sheep’ cycle was set up to determine whether feeding the progeny of these ticks on naïve sheep could lead to infection, and to compare clinical outcomes resulting from this transmission with those observed following infection by the natural A. variegatum (Av) vector. Using local strains of ticks (KIMINI-Rm and KIMINI-Av) and of E. ruminantium (BK242), we recorded, using the PCR technique, the presence of bacterial DNA in ticks (larvae for Av and females for Rm) engorged on sheep inoculated by BK242-infected blood. The bacterial DNA was also detected in the next stages of the lifecycle of R. microplus (eggs and larvae), and in sheep infested either by those R. microplus larvae or by A. variegatum nymphs moulted from larvae engorged on blood-inoculated sheep. Bacterial infection in these sheep was demonstrated by detecting antibodies to E. ruminantium using the MAP1-B ELISA and by isolation of the bacterium on cell culture from blood. The sequences of PCS20 gene detected in ticks and sheep were identical to that of the BK242 strain. Our results confirm that R. microplus can acquire and transmit E. ruminantium to the next stage. However, this transmission resulted in a mild subclinical disease whereas severe clinical disease was observed in sheep infested by A. variegatum infected nymphs, suggesting differences in the tick/bacteria relationship. Future studies will focus on replicating these findings with ticks of different isolates and life stages to determine if R. microplus is playing a role in the epidemiology of heartwater in West Africa. Additionally, studies will investigate whether sheep that are seropositive due to infestation by E. ruminantium-infected R. microplus are subsequently protected against heartwater. Such data will add to our understanding of the possible impact of R. microplus in areas where it has become recently established.
Published: 2023

49. Integrative taxonomy and phylogeny of leafless Vanilla orchids from the South‐West Indian Ocean region reveal two new Malagasy species

Author: Cathucia F. Andriamihaja, Alemao Botomanga, Chantal Misandeau, Aro V. Ramarosandratana, Michel Grisoni, Denis Da Silva, Thierry Pailler, Vololoniaina H. Jeannoda, Pascale Besse, 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), Université d'Antananarivo, Association Des Amis de la Forêt d’Ambodiriana-Manompana (ADAFAM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), We acknowledge all the institutions that have granted us research and collect permits: DREED of Madagascar, Madagascar National Parks, SAGE, Asity, Tsaranoro VOI, Bongolava Maitso, CFPF, ONG ADAFAM Ambodiriana funded by American Orchids Society (AOS) and Univet Nature, and and BRC Vatel for plant material. This research was financially and logistically supported by the University of Antananarivo, University of Reunion Island, CIRAD, and the UE-Feder-Interreg Project GerminationII-phase2. It was funded by a PhD grant to C. F. Andriamihaja from the European Regional Development Fund attributed by the Regional Council and from an Erasmus+ grant. A. V. Ramarosandratana and A. Botomanga also received a grant from Chanel Parfum Beauté for a conservation program of Vanilla species.
Subjects: Phylogénie, [SDV]Life Sciences [q-bio], Plant Science, phylogeography, F50 - Anatomie et morphologie des plantes, microsatellites, morphology, Madagascar, systematics, Vanilla, Ecology, Evolution, Behavior and Systematics, Morphologie végétale, F70 - Taxonomie végétale et phytogéographie, Taxonomie, species delimitation, Espèce nouvelle, ITS, Génotype
Abstract: Microsatellite data used to produce genetic structuring (Fig. 2) and PCoA (Fig. S3) are accessible on the online UMR PVBMT Cirad dataverse (https://doi.org/10.18167/DVN1/3OFMLH).; International audience; The leafless Vanilla species complex from the South-West Indian Ocean (SWIO) region has long been a taxonomic challenge, due to limited patterns of morphological differentiation and an absence of variation within chloroplast sequences. This complex includes seven known morphospecies: V. madagascariensis, V. bosseri, V. decaryana, and V. perrieri endemic to Madagascar, V. humblotii presumed as endemic to the Comoros Archipelago, but also present in Madagascar, V. roscheri from the East African coast, and V. phalaenopsis endemic to Seychelles. A previous population genetic study using microsatellite markers allowed us to distinguish, in addition to the five recognized Malagasy taxa, two other genetic clusters present in the East of the island. An integrative taxonomy approach was therefore conducted by combining microsatellite and morphological data used in the previous study with new data sets, and by adding ITS sequencing data, to validate the taxonomic level of these Malagasy genetic clusters and unravel phylogenetic relationships between SWIO species. As a result, based on phylogenetic, genotypic and morphological evidence, nine species were discriminated in the SWIO region, including seven in Madagascar, with two new eastern species. The leafless Vanilla group originated and diversified in Madagascar, from an ancestor of African descent, with three subsequent independent colonization events from Madagascar to the other territories of SWIO within the two main lineages (white versus yellow flower species). The new Malagasy species, V. allorgeae Andriamihaja & Pailler sp. nov., and V. atsinananensis Andriamihaja & Pailler sp. nov., are described and a new identification key is proposed.
Published: 2023

50. Clé d'identification des graines des principales adventices de La Réunion - version 1 - 55 espèces

Author: Schwartz, Marion, Etheve, Abel, Le Bourgeois, Thomas, Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), and Département Systèmes Biologiques (Cirad-BIOS)
Subjects: Identification, Clé de détermination, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Adventices, Adventices tropicales, Graines, La Réunion
Abstract: International audience; Les adventices représentent une contrainte majeure pour le développement des cultures, particulièrement en milieu tropical. L’étude de la biologie des adventices et une meilleure connaissance de leur comportement permettraient à terme une meilleure gestion de l’enherbement et une diminution de l’impact des produits phytosanitaires.Cette clé a pour but de caractériser et décrire les graines des principales adventices de La Réunion et de pouvoir déterminer l’espèce d’adventice correspondant à une graine récoltée ou ramassée dans une parcelle. Elle permetnotamment aux chercheurs, ingénieurs ou expérimentateurs de réaliser des expérimentations pour étudier et évaluer le stock semencier d’une parcelle.Cette clé est destinée à être complétée au fur et à mesure de la caractérisation des graines de nouvelles espèces d’adventices. Les versions de cette clé d’identification seront donc mises à jour au cours du temps
Published: 2023

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