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RPG Explorer : un outil pour comprendre les dynamiques d’occupation des terres agricole
No full text1. la description de l'outil : RPG Explorer est un logiciel développé pour analyser les dynamiques du paysage agricole à partir des données du Registre Parcellaire Graphique (RPG). Ces données, issues des déclarations PAC des agriculteurs, constituent une mine d’informations très importante pour décrire un territoire agricole mais elles nécessitent, en l’état, des compétences en SIG élevée pour les valoriser. RPG Explorer a été conçu pour faciliter le traitement aux agronomes non-spécialistes du SIG. Le logiciel permet, entre autres, de produire l’assolement d’un territoire pour chaque année, de lier les îlots des différences années pour reconstituer les séquences de culture et de modéliser les rotations par type d’exploitation ou par type de sol à partir des cultures observées. Les sorties de l’outil peuvent être exploitées sous tableur ou sous SIG. L’outil est amélioré grâce aux retours des utilisateurs. RPG explorer est un logiciel gratuit déposé auprès de l'Agence de Protection des Programmes. Il est développé au sein de l'UMR INRA AgroParisTech SAD-APT en collaboration avec d'autres équipes de recherche. Son développement a pu se faire grâce à des crédits ADEME et AFB/ONEMA. 2. les avantages et inconvénients de l'outil : RPG Explorer permet de répondre à bon nombre de questions d’ordre agronomique et environnemental liées à l’occupation du sol agricole (aire d’alimentation de captage (AAC), bassin versant ou bassin d’approvisionnement d’une culture par exemple). Les données RPG ne sont pas fournies avec l’exécutable de l’outil. RPG Explorer fonctionne avec les données RPG disponibles gratuitement (sans identifiants exploitation) sur le site de l’IGN (2015 à 2017), ces données sont très complètes d’un point de vue cultural (328 classes culturales). Les données avec identifiants exploitation ne sont accessibles qu’aux organisations en charge de mission de service public (accès gratuit auprès des DRAAF des territoires concernés). RPG Explorer tourne sur tous les PC mais fonctionne mieux avec une dizaine de Go de mémoire et un disque dur avec beaucoup de place (une centaine de Go de libre). Actuellement, des développements sont en cours pour adapter l’outil aux données RPG de niveau 2 diffusées par les DRAAF (2015 à 2017). 3. le degré d’opérationnalité de l’outil : RPG Explorer est totalement opérationnel et structuré en modules. Un premier module calcule les évolutions de l’assolement et des caractéristiques des exploitations agricoles (nombre d’exploitation, SAU de l’exploitation et type d’exploitation). Un second module génère les séquences de cultures pour chaque îlot d’un territoire. Un troisième module identifie les principales séquences de cultures et modélise les rotations d’un territoire. L’outil peut traiter les données RPG de la France métropolitaine et DOM/TOM de 2006 à 2017. La prise en charge des données exploitation post 2014 ne sera effective que lorsque les fichiers transmis pas les DRAAF seront standardisés (discussions en cours). 4. les moyens de mise en oeuvre de l’outil L’outil est facile d’installation (exécutable envoyé sur demande). La prise en main de l’outil se fait par auto-formation (notice et support PPT et vidéos à disposition) ou en participant à des formations (de 2 à 4 par an). Une hot line est assurée par mail. 5. un exemple d'application concret : RPG Explorer a été utilisé sur des AAC, pour extraire les couples précédent/suivant des bases du RPG ainsi que leur proportion pour chaque type de sol pour alimenter la matrice technique mobilisée dans l’approche Coclick’Eau. RPG Explorer a été mis en oeuvre sur 4 territoires pilotes afin de calculer les assolements de rotation par type de sol et contribuer au calcul du stockage de carbone dans les sols (projet ADEME ABC’Terre)
Ability of a soil-vegetation-atmosphere transfer model and a two-source energy balance model to predict evapotranspiration for several crops and climate conditions
No full textThe heterogeneity of Agroecosystems, in terms of hydric conditions, crop types and states, and meteorological forcing, is difficult to characterize precisely at the field scale over an agricultural landscape. This study aims to perform a sensitivity study with respect to the uncertain model inputs of two classical approaches used to map the evapotranspiration of agroecosystems: (1) a surface energy balance (SEB) model, the Two-Source Energy Balance (TSEB) model, forced with thermal infrared (TIR) data as a proxy for the crop hydric conditions, and (2) a soil- vegetation-atmosphere transfer (SVAT) model, the SEtHyS model, where hydric conditions are computed from a soil water budget. To this end, the models' skill was compared using a large and unique in situ database covering different crops and climate conditions, which was acquired over three experimental sites in southern France and Morocco. On average, the models provide 30 min estimations of latent heat flux (LE) with a RMSE of around 55 W m(-2) for TSEB and 47 W m(-2) for SEtHyS, and estimations of sensible heat flux (H) with a RMSE of around 29 W m(-2) for TSEB and 38 W m(-2) for SEtHyS. A sensitivity analysis based on realistic errors aimed to estimate the potential decrease in performance induced by the spatialization process. For the SVAT model, the multi-objective calibration iterative procedure (MCIP) is used to determine and test different sets of parameters. TSEB is run with only one set of parameters and provides acceptable performance for all crop stages apart from the early growing season (LAI 0.8 m(2)m(-2)) and unstressed conditions, using sets of parameters that only differentiate crop types is a valuable trade-off for SEtHyS. This study provides some scientific elements regarding the joint use of both approaches and TIR imagery, via the development of new data assimilation and calibration strategies
Accumulation during fruit development of components of interest in seed of Chia (Salvia hispanica L.) cultivar Oruro (c) released in France star
No full textThis study aimed to examine the accumulation of oil, fatty acids, sterols and tocopherols contents and compositions during fruit development on the new cultivar of Chia Oruro (Panam Cie, France) cultivated in France. This cultivar is the first released genotype in Europe and for cultivation in Europe. The experiment was conducted in 2017, in south-western France at the Regional centre for organic agriculture, at Auch (near Toulouse, South-West of France). Four samplings were made at 17, 24, 27 and 35 days after flowering (DAF). These dates of sampling correspond to stages 7-8 (fruit development and maturity) of BBCH scale. Oil content, fatty acid composition and sterols and tocopherols contents and profiles were determined. The highest levels of oil and tocopherols were reached at 27 DAF. In contrast, phytosterols content was highest at 17 DAF (726.2 mg/100 g of oil) and decreased after this date. beta-sitosterol was the main sterol in chia seed (63.4 to 89.1% of total sterols, depending of stage of fruit development). gamma-tocopherol represented more than 92% of the total tocopherols present in the seed. High levels of polyunsaturated fatty acids (74.4 to 80% of total fatty acids) were observed in our study confirming those already reported in this species. High levels of saturated and monounsaturated fatty acids were reported at earlier stages and decreased gradually during fruit development. Polyunsaturated fatty acids followed an opposite trend. Their level was lowest at 17 DAF (74.4%) and increased gradually to reach their higher level at 35 DAF (80%). These results suggested clearly the interest to harvest and use of seed before entire maturity of the grain.Cette étude a examiné l’accumulation de l’huile, des acides gras, des stérols et des tocophérols durant le développement du fruit du nouveau cultivar de Chia Oruro (Panam Cie, France) cultivé en France. Ce cultivar est le premier génotype sélectionné en Europe et pour l’Europe. L’expérimentation a été réalisée en 2017, dans le sud-ouest de la France, au Centre régional d’expérimentation en agriculture biologique, à Auch (près de Toulouse, dans le sud-ouest de la France). Quatre prélèvements ont été effectués 17, 24, 27 et 35 jours après la floraison (DAF). Ces dates d’échantillonnage correspondent aux stades 7–8 (développement du fruit et maturité) de l’échelle BBCH. La teneur en huile, la composition en acides gras et les teneurs et profils en stérols et en tocophérols ont été déterminés. Les teneurs les plus élevées d’huile et de tocophérols ont été atteintes à 27DAF. Au contraire, la teneur en phytostérols était la plus élevée à 17DAF (726,2 mg/100 g d’huile) et a diminué après cette date. Le b-sitostérol a été le principal stérol contenu dans les graines de chia (63,4 to 89,1% des stérols totaux et en fonction du stade de développement du fruit). Le g-tocophérol représente plus de 92% du total des tocophérols présents dans la graine. Des teneurs élevées d’acides gras polyinsaturés (74,4 à 80% des acides gras totaux) ont été observées dans notre étude, ce qui confirme celles déjà signalées chez cette espèce. Des teneurs plus élevées d’acides gras saturés et mono-insaturés ont été observées aux stades précoces du développement du fruit et ont diminué progressivement au cours de la maturation. Les acides gras
polyinsaturés ont suivi une tendance opposée. Leur niveau était le plus bas à 17DAF (74,4 %) et a augmenté progressivement pour atteindre leur niveau supérieur à 35DAF (80 %). Ces résultats suggèrent clairement l’intérêt de récolter et d’utiliser les graines avant leur maturité complète
Analyse génétique de la « fromageabilité » du lait de vache prédite par spectrométrie dans le moyen infrarouge en race Montbéliarde
No full textThe olfactory secretome varies according to season in female sheep and goat
No full textBackground: Small ungulates (sheep and goat) display a seasonal breeding, characterised by two successive periods, sexual activity (SA) and sexual rest (SR). Odours emitted by a sexually active male can reactivate the ovulatory cycle of anoestrus females. The plasticity of the olfactory system under these hormonal changes has never been explored at the peripheral level of odours reception. As it was shown in pig that the olfactory secretome (proteins secreted in the nasal mucus) could be modified under hormonal control, we monitored its composition in females of both species through several reproductive seasons, thanks to a non-invasive sampling of olfactory mucus. For this purpose, two-dimensional gel electrophoresis (2D-E), western-blot with specific antibodies, MALDI-TOF and high-resolution (nano-LC-MS/MS) mass spectrometry, RACE-PCR and molecular modelling were used.
Results: In both species the olfactory secretome is composed of isoforms of OBP-like proteins, generated by post-translational modifications, as phosphorylation, N-glycosylation and O-GlcNAcylation. Important changes were observed in the olfactory secretome between the sexual rest and the sexual activity periods, characterised in ewe by the specific expression of SAL-like proteins and the emergence of OBPs O-GlcNAcylation. In goat, the differences between SA and SR did not come from new proteins expression, but from different post-translational modifications, the main difference between the SA and SR secretome being the number of isoforms of each protein. Proteomics data are available via ProteomeXchange with identifier PXD014833.
Conclusion: Despite common behaviour, seasonal breeding, and genetic resources, the two species seem to adapt their olfactory equipment in SA by different modalities: the variation of olfactory secretome in ewe could correspond to a specialization to detect male odours only in SA, whereas in goat the stability of the olfactory secretome could indicate a constant capacity of odours detection suggesting that the hallmark of SA in goat might be the emission of specific odours by the sexually active male. In both species, the olfactory secretome is a phenotype reflecting the physiological status of females, and could be used by breeders to monitor their receptivity to the male effect
Ecosystem Services and Importance of Common Tree Species in Coffee-Agroforestry Systems: Local Knowledge of Small-Scale Farmers at Mt. Kilimanjaro, Tanzania
No full textResearch Highlights: Global coffee production, especially in smallholder farming systems, is vulnerable and must adapt in the face of climate change. To this end, shaded agroforestry systems are a promising strategy. Background and Objectives: Understanding local contexts is a prerequisite for designing locally tailored systems; this can be achieved by utilizing farmers' knowledge. Our objective is to explore ecosystem services (ESs) provided by different shade tree species as perceived by farmers and possible factors (elevation, gender, and membership in local farmers groups) influencing these perceptions. We related these factors, as well as farmers' ESs preferences, to planting densities of tree species. Materials and Methods: During interviews with 263 small-scale coffee farmers on the southern slope of Mt. Kilimanjaro, they ranked the most common shade tree species according to perceived provision of the locally most important ESs for coffee farmers. We asked them to estimate the population of each tree species on their coffee fields and to identify the three ESs most important for their household. Results: Food, fodder, and fuelwood emerged as the most important ESs, with 37.8% of the respondents mentioning all three as priorities. Density of tree species perceived to provide these three ESs were significantly higher for farmers prioritizing these services compared to farmers that did not consider all three ESs in their top three. Albizia schimperiana scored the highest for all rankings of regulatory ESs such as coffee yield improvement, quality shade provision, and soil fertility improvement. Influence of elevation, gender, and farmer group affiliation was negligible for all rankings. Conclusions: This study shows the need to understand factors underlying farmers' management decisions before recommending shade tree species. Our results led to the upgrade of the online tool (shadetreeadvice.org) which generates lists of potential common shade tree species tailored to local ecological context considering individual farmers' needs
Estimation of plant and canopy architectural traits using the D3P Digital Plant Phenotyping Platform
No full textThe extraction of desirable heritable traits for crop improvement from high-throughput phenotyping (HTP) observations remains challenging. We developed a modeling workflow named Digital Plant Phenotyping Platform, D3P, to access crop architectural traits from HTP observations. D3P couples the ADEL (architectural model of development based on L-systems) wheat (Triticum aestivum) model, that describes the time course of the three-dimensional architecture of wheat crops, with simulators of images acquired with HTP sensors. We demonstrated that a sequential assimilation of the green fraction derived from RGB (Red Green Blue) images of the crop into D3P provides accurate estimates of five key parameters (phyllochron, lamina length of the first leaf, rate of elongation of leaf lamina, number of green leaves at the start of leaf senescence and minimum number of green leaves) of the ADEL-Wheat model that drive the time course of green area index and the number of axes with more than three leaves at the end of the tillering period. However, leaf and tiller orientation and inclination characteristics were poorly estimated. D3P was also used to optimize the observational configuration. The results, obtained from in silico experiments conducted on wheat crops at several vegetative stages, showed that the accessible traits could be estimated accurately with observations made at 0{degree sign} and 60{degree sign} zenith view inclination with a temporal frequency of 100 {degree sign}Cd. This illustrates the potential of the proposed holistic approach that integrates all the available information into a consistent system for interpretation. The potential benefits and limitations of the approach are further discussed
CR3 engaged by PGL-I triggers Syk-calcineurin-NFATc to rewire the innate immune response in Leprosy.
No full textMycobacterium leprae, the causative agent of leprosy, is unique amongst human pathogens in its capacity to produce the virulence factor phenolic glycolipid (PGL)-I. In addition to mediating bacterial tropism for neurons, PGL-I interacts with Complement Receptor (CR)3 on macrophages (MPs) to promote infection. We demonstrate here that PGL-I binding to CR3 also enhances bacterial invasion of both polymorphonuclear neutrophils (PMNs) and dendritic cells (DCs). Moreover, in all cell types CR3 engagement by PGL-I activates the Syk tyrosine kinase, inducing calcineurin-dependent nuclear translocation of the transcription factor NFATc. This selectively augments the production of IL-2 by DCs, IL-10 by PMNs and IL-1β by MPs. In intranasally-infected mice PGL-I binding to CR3 heightens mycobacterial phagocytosis by lung PMNs and MPs, and stimulates NFATc-controlled production of Syk-dependent cytokines. Our study thus identifies the CR3-Syk-NFATc axis as a novel signaling pathway activated by PGL-I in innate immune cells, rewiring host cytokine responses to M. leprae
