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Application of near-infrared spectroscopy for fast germplasm analysis and classification in multi-environment using intact-seed peanut(Arachis hypogaea L.)

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Oil Crop Science 2024年第2期9卷 132-141页

作者： Fentanesh Chekole Kassie Gilles Chaix Hermine Bille Ngalle Maguette Seye Coura Fall Hodo-Abalo Tossim Aissatou Sambou Olivier Gibert Fabrice Davrieux Joseph Martin Bell Jean-Francois Rami Daniel Fonceka Joel Romaric Nguepjop Department of Plant Biology and Physiology Faculty of SciencesUniversity of Yaounde IYaoundeP.O.Box 337Cameroon Department of Plant Science College of AgricultureWolaita Sodo UniversitySodoP.O.Box 138Ethiopia CIRAD UMR AGAP InstitutMontpellierFrance AGAP Institut Univ MontpellierCIRADINRAEInstitut AgroMontpellierFrance ChemHouse Research Group MontpellierFrance Centre D’Etudes Regional Pour L’Amelioration de L’Adaptation a La Secheresse(CERAAS/ISRA) Route de KhomboleThiesBP 3320Senegal Dispositif de Recherche et de Formation en Partenariat Innovation et Amelioration Varietale en Afrique de L’Ouest(IAVAO)CERAASRoute de KhomboleThiesBP 3320Senegal CIRAD UMR QUALISUDSaint PierreFrance

Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional *** this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess germplasm variability from whole seed of 699 samples,field-collected and assembled in four genetic and environmentbased sets:one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population,evaluated in three environments in a large spatial scale of two countries,Mbalmayo and Bafia in Cameroon and Nioro in Senegal,under rainfed *** elemental spectra were gathered on six subsets of seeds of each sample,after three rotation scans,with a spectral resolution of 16 cm-1over the spectral range of867 nm to 2530 *** were then processed by principal component analysis(PCA)coupled with Partial least squares-discriminant analysis(PLS-DA).As results,a huge variability was found between varieties and genotypes for all NIR wavelength within and between *** magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 nm,usually related to oil content and fatty acid *** yielded the most chemical attributes in three significant PCs(i.e.,eigenvalues>10),which together captured 93%of the total variation,revealing genetic and environment structure of varieties and genotypes into four clusters,corresponding to the four samples *** pattern of genetic variability of the interspecific population covers,remarkably half of spectrum of the core-collection,turning out to be the ***,a PLS-DA model was developed and a strong accuracy of 99.6%was achieved for the four sets,aiming to classify each seed sample according to environment *** confusion matrix achieved for the two sets of Bafia and Nioro showed 100%of instances classified correctly with 100%at both sensitivity and specificity,confirming that their seed quality was different f

关键词： Groundnut Oilseed Near infrared spectroscopy Germplasm analysis Environment Nutritional Breeding

Concept and application of ideal protein for pigs

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Journal of Animal Science and Biotechnology 2015年第3期6卷 269-279页

作者： Jaap van Milgen Jean-Yves Dourmad INRA agrocampus ouest

Knowledge about the amino acid requirements and the response of pigs to the amino acid supply is essential in feed formulation. A deficient AA supply results in a reduction in performance while an oversupply is costly and leads to excessive nitrogen excretion with a potentially negative environmental impact. Amino acid requirements are determined to a large extent by the protein deposition in the body and, for lactating sows, by the protein exported in the milk. The concept of ideal protein was developed more than 50 years ago and refers to a protein with an amino acid profile that exactly meets the animal＇s requirement so that all amino acids are equally limiting for performance. Because Lys typically is the first-limiting amino acid, the ideal amino acid profile is often expressed relative to Lys. Although the ideal protein profile is often assumed to be constant for a given production stage, （small） changes in the ideal protein profile can occur within a production stage. This can be caused by changes in the relative contribution of the different components of amino acid requirements during the productive life on the animal （e.g. changes in the relative contribution of growth and maintenance）. Amino acids requirements can be determined experimentally using dose-response studies. The design of the study, the chosen response criterion, and the statistical model affect the requirement estimate. Although considerable experimental work has been carried out to determine the requirements for Lys, Met, Thr, and Trp in growing pigs （and to a lesser extent in sows）, little is known about the requirements for the other essential amino acids. Experimental dose-response studies generally focus on the requirement and less on the overall response （i.e. what are the consequences of an amino acid deficiency？）. This latter aspect is, to some extent, accounted for in modelling approaches that quantify the response of the animal to the amino acid supply in a dynamic way. The paper d

关键词： Amino acids Gestation Growth Ideal protein Lactation Modeling Pigs

First-wave COVID-19 daily cases obey gamma law

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Infectious Disease Modelling 2022年第2期7卷 64-74页

作者： Jean Duchesne Olivier A.Coubard agrocampus ouest 2 rue Andre Le Notre49000AngersFrance The Neuropsychological Laboratory CNS-Fed240 rue de Rivoli75001ParisFrance

Modelling how a pandemic is spreading over time is a challenging *** new coronavirus disease called COVID-19 does not escape this rule as it has embraced over two hundred *** for previous pandemics,several studies have attempted to model the occurrence of cases caused by ***,no study has succeeded in accurately modelling the impact of the infectious *** we show that COVID-19 daily case distribution in humans obeys a Gamma law,which two new parameters can describe without any *** the Gamma law has been exploited for nearly two centuries to describe the statistical distribution of spatial or temporal quantities,the goodness-of-fit rationale using two or three parameters has remained *** new Gamma law approach we demonstrate here emerges from actual data and sheds light on the underlying mechanisms of the observed *** finding has promising applicability in the epidemiological domain and in all disciplines involving branching systems,for which our Gamma law approach may bring a solution to hitherto unsolved problems.

关键词： COVID-19 Epidemiology Gamma law Humans Statistical physics

Effects of flight parameters for plant protection UAV on droplets deposition rate based on a 3D simulation approach

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International Journal of Agricultural and Biological Engineering 2023年第1期16卷 66-72页

作者： Lifeng Xu Zhongzhu Yang Zusheng Huang Weilong Ding Gerhard Buck-Sorlin College of Computer Science&Technology Zhejiang University of TechnologyHangzhou 310026China IRHS INRAEAGROCAMPUS OUESTUniversite d’AngersSFR 4207 QUASAV42 rue Georges Morel49071 BeaucouzécedexFrance

With the development of aviation agricultural technology,the number of farmers adopting the use of drones in daily agricultural activities is growing rapidly in recent *** these,a large portion constitutes agricultural drones being used in pest control and crop protection practices,*** spraying of *** pesticides with drones have proven to be faster than other traditional *** the downside,flight time and range of Unmanned Aerial Vehicles(UAV)are often ***,a proper arrangement of flight height and velocity will greatly improve spraying efficiency.A new strategy to optimize the flight parameters,*** height and flight velocity,for fixed-wing UAV with a 3D simulation-based approach together with an automatic optimization algorithm was proposed in this *** find the optimal parameters for a UAV to fly and spray under certain environmental conditions,a three-dimensional model of the target crop was established first,followed by a detailed simulation of droplet *** a demonstration case,a grass model was developed and used as the target plant,and a physics-based method was used to simulate realistically the movement of the droplets in the air as well as the interaction between the droplets and the plant to obtain the droplet deposition rate under the specified operating ***,the standard Particle Swarm Optimization(PSO)algorithm was used to optimize the UAV operating parameters to obtain the best operating *** results indicate that using the standard PSO algorithm to optimize the operating parameters of the drone could significantly improve the deposition rate and find the best operating parameters.

关键词： unmanned aerial vehicle droplet deposition 3D simulation particle swarm optimization algorithm

Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect？ A demonstration in oilseed rape

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Insect Science 2017年第6期24卷 1045-1056页

作者： Tom Lachaise Morgane Ourry Lionel Lebreton Anne-Yvonne Guillerm-Erckelboudt Juliette Linglin Chrystelle Paty Valerie Chaminade Nathalie Marnet Julie Aubert Denis Poinsot Anne-Marie Cortesero Christophe Mougel IGEPP Agrocampus Ouest INRA Universite de Rennes 1 Le Rheu France IGEPP Agrocampus Ouest INRA Universite de Rennes 1 Universite Bretagne-Loire Rennes France INRA UR1268 BIA-Le Rheu France INRA-AgroParisTech UMR 518 Applied Mathematics and Computer Sciences-Paris France

Interactions between plants and phytophagous insects play an important part in shaping the biochemical composition of plants. Reciprocally plant metabolites can influ- ence major life history traits in these insects and largely contribute to their fitness. Plant rhizospheric microorganisms are an important biotic factor modulating plant metabolites and adaptation to stress. While plant-insects or plant-microorganisms interactions and their consequences on the plant metabolite signature are well-documented, the impact of soil microbial communities on plant defenses against phytophagous insects remains poorly known. In this study, we used oilseed rape （Brassica napus） and the cabbage root fly （Delia radicum） as biological models to tackle this question. Even though D. radicum is a belowground herbivore as a larva, its adult life history traits depend on aboveground signals. We therefore tested whether soil microbial diversity influenced emergence rate and fitness but also fly oviposition behavior, and tried to link possible effects to modifications in leaf and root metabolites. Through a removal-recolonization experiment, 3 soil microbial modalities （＂high,＂＂medium,＂＂low＂） were established and assessed through amplicon sequencing of 16S and 18S ribosomal RNA genes. The ＂medium＂ modality in the rhizosphere significantly improved insect development traits. Plant-microorganism interactions were marginally associated to modulations of root metabolites profiles, which could partly explain these results. We highlighted the potential role of plant-microbial interaction in plant defenses against Delia radicum. Rhizospheric microbial communities must be taken into account when analyzing plant defenses against herbivores, being either below or aboveground.

关键词： Brassica napus Delia radicum life history traits plant primary and secondary metabolites rhizophagous pest soil microbial diversity

Soil properties, grassland management, and landscape diversity drive the assembly of earthworm communities in temperate grasslands

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Pedosphere 2021年第3期31卷 375-383页

作者： Kevin HOEFFNER Mathieu SANTONJA CécileMONARD Lou BARBE Mathilde LEMOING Daniel CLUZEAU University of Rennes CNRSECOBIO UMR 6553Rennes F-35000France INRAE AGROCAMPUS OUEST UMR SASRennes F-35000France Aix Marseille Université Avignon UniversitéCNRSIRDIMBEMarseille F-13397France

Earthworms are widespread soil organisms that contribute to a wide range of ecosystem *** such,it is important to improve our knowledge,still scanty,of the factors that drive the assembly of earthworm *** aim of the present study was to conjointly evaluate the effects on the assembly of earthworm communities of i)soil properties(texture,organic matter content,and pH),ii)grassland management(grassland age,livestock unit,and type of fertilization),iii)landscape diversity(richness,diversity of surrounding habitats,and grassland plant diversity),and iv)presence of *** study was conducted in temperate grasslands of Brittany,*** were sampled in 24 grasslands and,in three of these grasslands,they were sampled near a hedgerow or near a ditch(control without a hedgerow).Soil properties explained the larger portion of the variation in the earthworm community parameters compared to grassland management or landscape *** increase in soil organic matter content and pH were the most favorable factors for earthworm abundance and biomass,in particular for endogeic *** grassland management,the increase in the livestock unit was the most damaging factor for earthworm communities,in particular for the anecic earthworm biomass and endogeic species ***,landscape diversity negatively affected the total earthworm abundance and epigeic earthworm biomass,but it was related to an increase in the epi-anecic *** a finer scale,we also demonstrated that the presence of hedgerows surrounding grasslands enhanced earthworm species richness,especially within the epigeic and anecic ecological *** study highlights that the earthworm ecological categories respond specifically to environmental filters;further studies need to be conducted to elucidate the factors that drive the assembly of earthworm communities at this ecological category *** recommend that policymakers should act on landscape man

关键词： ecological categoryfield marginhedgerowlivestock unitsoil organic mattersoil PHtrampling

FSPM-P： towards a general functional-structural plant model for robust and comprehensive model development

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Frontiers of Computer Science 2016年第6期10卷 1103-1117页

作者： Michael HENKE Winfried KURTH Gerhard H. BUCK-SORLIN Department of Ecoinformatics Biometrics and Forest Growth University of Gottingen Gottingen 37077 Germany umr1345 Institut de Recherche en Horticulture et Semences (IRHS) AGROCAMPUS OUEST Centre d'Angers Angers 49045 France

In the last decade, functional-structural plant modelling （FSPM） has become a more widely accepted paradigm in crop and tree production, as 3D models for the most important crops have been proposed. Given the wider portfolio of available models, it is now appropriate to enter the next level in FSPM development, by introducing more efficient methods for model development. This includes the consideration of model reuse （by modularisafion）, combination and comparison, and the enhancement of existing mod- els. To facilitate this process, standards for design and communication need to be defined and established. We present a first step towards an efficient and general, i.e., not speciesspecific FSPM, presently restricted to annual or bi-annual plants, but with the potential for extension and further generalization. Model structure is hierarchical and object-oriented, with plant organs being the base-level objects and plant individual and canopy the higher-level objects. Modules for the majority of physiological processes are incorporated, more than in other platforms that have a similar aim （e.g., photosynthesis, organ formation and growth）. Simulation runs with several general parameter sets adopted from the literature show that the present prototype was able to reproduce a plausible output range for different crops （rapeseed, barley, etc.） in terms of both the dynamics and final values （at harvest time） of model state variables such as assimilate production, organ biomass, leaf area and architecture.

关键词： functional-structural plant model prototyping,modelling standards teaching / learning FSPM GroIMP

Consequences of coinfection with protective symbionts on the host phenotype and symbiont titres in the pea aphid system

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Insect Science 2017年第5期24卷 798-808页

作者： Melanie Leclair Sarah Polin Thibaut Jousseaume Jean-Christophe Simon Akiko Sugio Stephanie Morliere Takema Fukatsu Tsutomu Tsuchida Yannick Outreman IGEPP Agrocampus Ouest INRA Universite de Rennes 1 Universite Bretagne-Loire Rennes France IGEPP Agrocampus OuestINRA Universit6 de Rennes 1 Le Rheu France Bioproduction Research Institute AIST Tsukuba Japan Graduate School of Science and Engineering University of Toyama Toyama Japan

Symbiotic associations between microbes and insects are widespread, and it is frequent that several symbionts share the same host individual. Hence, interactions can occur between these symbionts, influencing their respective abundance within the host with consequences on its phenotype. Here, we investigate the effects of multiple infections in the pea aphid, Acyrthosiphon pisurn, which is the host of an obligatory and several facultative symbionts. In particular, we study the influence of a coinfection with 2 protective symbionts： Harniltonella defensa, which confers protection against parasitoids, and Rickettsiella viridis, which provides protection against fungal pathogens and predators. The effects of Hamiltonella-Rickettsiella coinfection on the respective abundance of the symbionts, host fitness and efficacy of enemy protection were studied. Asymmetrical interactions between the 2 protective symbionts have been found： when they coinfect the same aphid individuals, the Rickettsiella infection affected Hamiltonella abundance within hosts but not the Hamiltonella-mediated protective phenotype while the Hamiltonella infection negatively influences the Rickettsiella-mediated protective phenotype but not its abundance. Harboring the 2 protective symbionts also reduced the survival and fecundity of host individuals. Overall, this work highlights the effects of multiple infections on symbiont abundances and host traits that are likely to impact the maintenance of the symbiotic associations in natural habitats.

关键词： Acyrthosiphon pisum Hamiltonella defensa host fitness multiple infections protective symbionts symbiont abundance

The promises and challenges of research on plant-insect-microbe interactions

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Insect Science 2017年第6期24卷 904-909页

作者： Jean-Christophe Simon Arjen Biere Akiko Sugio umr 1349 Institut de Genetique Environnement et Protection des Plantes INRA Agrocampus Ouest Universite Rennes 1 Domaine de la Motte Le Rheu Cedex France Department of Terrestrial Ecology Netherlands Institute of Ecology NIOO-KNA W Wageningen the Netherlands

Ecological interactions are of paramount importance for the functioning and health of ecosystems. Phytophagous insects are part of complex ecological networks involving abiotic factors, host plants, natural enemies, and benefi- cial organisms （McLean et al., 2016）. Insects and plants are also associated durably or transitorily with a wealth of microbes including pathogens, commensals and beneficial partners from a vast array of microbial taxa （Sugio et al., 2015）. In recent years, evidence has accumulated that microbes directly or indirectly influence plant-insect interactions at individual, population and community levels.

关键词： SYMBIONTS FUNGI