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Van Oijen, M., & Höglind, M. (2016). Toward a Bayesian procedure for using process-based models in plant breeding, with application to ideotype design. Euphytica, 207(3), 627–643.
Abstract: Process-based grassland models (PBMs) simulate growth and development of vegetation over time. The models tend to have a large number of parameters that represent properties of the plants. To simulate different cultivars of the same species, different parameter values are required. Parameter differences may be interpreted as genetic variation for plant traits. Despite this natural connection between PBMs and plant genetics, there are only few examples of successful use of PBMs in plant breeding. Here we present a new procedure by which PBMs can help design ideotypes, i.e. virtual cultivars that optimally combine properties of existing cultivars. Ideotypes constitute selection targets for breeding. The procedure consists of four steps: (1) Bayesian calibration of model parameters using data from cultivar trials, (2) Estimating genetic variation for parameters from the combination of cultivar-specific calibrated parameter distributions, (3) Identifying parameter combinations that meet breeding objectives, (4) Translating model results to practice, i.e. interpreting parameters in terms of practical selection criteria. We show an application of the procedure to timothy (Phleum pratense L.) as grown in different regions of Norway.
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Eza, U., Shtiliyanova, A., Borras, D., Bellocchi, G., Carrère, P., & Martin, R. (2015). An open platform to assess vulnerabilities to climate change: An application to agricultural systems. Ecological Informatics, 30, 389–396.
Abstract: Numerous climate futures are now available from global climate models. Translation of climate data such as precipitation and temperatures into ecologically meaningful outputs for managers and planners is the next frontier. We describe a model-based open platform to assess vulnerabilities of agricultural systems to climate change on pixel-wise data. The platform includes a simulation modeling engine and is suited to work with NetCDF format of input and output files. In a case study covering a region (Auvergne) in the Massif Central of France, the platform is configured to characterize climate (occurrence of arid conditions in historical and projected climate records), soils and human management, and is then used to assess the vulnerability to climate change of grassland productivity (downscaled to a fine scale). We demonstrate how using climate time series, and process-based simulations vulnerabilities can be defined at fine spatial scales relevant to farmers and land managers, and can be incorporated into management frameworks. (C) 2015 Elsevier B.V. All rights reserved.
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Ben Touhami, H., & Bellocchi, G. (2015). Bayesian calibration of the Pasture Simulation model (PaSim) to simulate European grasslands under water stress. Ecological Informatics, 30, 356–364.
Abstract: As modeling becomes a more widespread practice in the agro-environmental sciences, scientists need reliable tools to calibrate models against ever more complex and detailed data. We present a generic Bayesian computation framework for grassland simulation, which enables parameter estimation in the Bayesian formalism by using Monte Carlo approaches. We outline the underlying rationale, discuss the computational issues, and provide results from an application of the Pasture Simulation model (PaSim) to three European grasslands. The framework was suited to investigate the challenging problem of calibrating complex biophysical models to data from altered scenarios generated by precipitation reduction (water stress conditions). It was used to infer the parameters of manipulated grassland systems and to assess the gain in uncertainty reduction by updating parameter distributions using measurements of the output variables.
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Ma, S., Lardy, R., Graux, A. - I., Ben Touhami, H., Klumpp, K., Martin, R., et al. (2015). Regional-scale analysis of carbon and water cycles on managed grassland systems. Env. Model. Softw., 72, 356–371.
Abstract: Predicting regional and global carbon (C) and water dynamics on grasslands has become of major interest, as grasslands are one of the most widespread vegetation types worldwide, providing a number of ecosystem services (such as forage production and C storage). The present study is a contribution to a regional-scale analysis of the C and water cycles on managed grasslands. The mechanistic biogeochemical model PaSim (Pasture Simulation model) was evaluated at 12 grassland sites in Europe. A new parameterization was obtained on a common set of eco-physiological parameters, which represented an improvement of previous parameterization schemes (essentially obtained via calibration at specific sites). We found that C and water fluxes estimated with the parameter set are in good agreement with observations. The model with the new parameters estimated that European grassland are a sink of C with 213 g C m(-2) yr(-1), which is close to the observed net ecosystem exchange (NEE) flux of the studied sites (185 g C m(-2) yr(-1) on average). The estimated yearly average gross primary productivity (GPP) and ecosystem respiration (RECO) for all of the study sites are 1220 and 1006 g C m(-2) yr(-1), respectively, in agreement with observed average GPP (1230 g C m(-2) yr(-1)) and RECO (1046 g C m(-2) yr(-1)). For both variables aggregated on a weekly basis, the root mean square error (RMSE) was similar to 5-16 g C week(-1) across the study sites, while the goodness of fit (R-2) was similar to 0.4-0.9. For evapotranspiration (ET), the average value of simulated ET (415 mmyr(-1)) for all sites and years is close to the average value of the observed ET (451 mm yr(-1)) by flux towers (on a weekly basis, RMSE similar to 2-8 mm week(-1); R-2 = 0.3-0.9). However, further model development is needed to better represent soil water dynamics under dry conditions and soil temperature in winter. A quantification of the uncertainties introduced by spatially generalized parameter values in C and water exchange estimates is also necessary. In addition, some uncertainties in the input management data call for the need to improve the quality of the observational system.
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Pulina, A., Lai, R., Salis, L., Seddaiu, G., Roggero, P. P., & Bellocchi, G. (2018). Modelling pasture production and soil temperature, water and carbon fluxes in Mediterranean grassland systems with the Pasture Simulation Model. Grass Forage Sci., 73(2), 272–283.
Abstract: Grasslands play important roles in agricultural production and provide a range of ecosystem services. Modelling can be a valuable adjunct to experimental research in order to improve the knowledge and assess the impact of management practices in grassland systems. In this study, the PaSim model was assessed for its ability to simulate plant biomass production, soil temperature, water content, and total and heterotrophic soil respiration in Mediterranean grasslands. The study site was the extensively managed sheep grazing system at the Berchidda‐Monti Observatory (Sardinia, Italy), from which two data sets were derived for model calibration and validation respectively. A new model parameterization was derived for Mediterranean conditions from a set of eco‐physiological parameters. With the exception of heterotrophic respiration (Rh), for which modelling efficiency (EF) values were negative, the model outputs were in agreement with observations (e.g., EF ranging from ~0.2 for total soil respiration to ~0.7 for soil temperature). These results support the effectiveness of PaSim to simulate C cycle components in Mediterranean grasslands. The study also highlights the need of further model development to provide better representation of the seasonal dynamics of Mediterranean annual species‐rich grasslands and associated peculiar Rh features, for which the modelling is only implicitly being undertaken by the current PaSim release.
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