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Rötter, R. P., Tao, F., Höhn, J. G., & Palosuo, T. (2015). Use of crop simulation modelling to aid ideotype design of future cereal cultivars. J. Experim. Bot., 66(12), 3463–3476.
Abstract: A major challenge of the 21st century is to achieve food supply security under a changing climate and roughly a doubling in food demand by 2050 compared to present, the majority of which needs to be met by the cereals wheat, rice, maize, and barley. Future harvests are expected to be especially threatened through increased frequency and severity of extreme events, such as heat waves and drought, that pose particular challenges to plant breeders and crop scientists. Process-based crop models developed for simulating interactions between genotype, environment, and management are widely applied to assess impacts of environmental change on crop yield potentials, phenology, water use, etc. During the last decades, crop simulation has become important for supporting plant breeding, in particular in designing ideotypes, i.e. ‘model plants’, for different crops and cultivation environments. In this review we (i) examine the main limitations of crop simulation modelling for supporting ideotype breeding, (ii) describe developments in cultivar traits in response to climate variations, and (iii) present examples of how crop simulation has supported evaluation and design of cereal cultivars for future conditions. An early success story for rice demonstrates the potential of crop simulation modelling for ideotype breeding. Combining conventional crop simulation with new breeding methods and genetic modelling holds promise to accelerate delivery of future cereal cultivars for different environments. Robustness of model-aided ideotype design can further be enhanced through continued improvements of simulation models to better capture effects of extremes and the use of multi-model ensembles.
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Porter, J. R., & Christensen, S. (2013). Deconstructing crop processes and models via identities. Plant Cell and Environment, 36(11), 1919–1925.
Abstract: This paper is part review and part opinion piece; it has three parts of increasing novelty and speculation in approach. The first presents an overview of how some of the major crop simulation models approach the issue of simulating the responses of crops to changing climatic and weather variables, mainly atmospheric CO2 concentration and increased and/or varying temperatures. It illustrates an important principle in models of a single cause having alternative effects and vice versa. The second part suggests some features, mostly missing in current crop models, that need to be included in the future, focussing on extreme events such as high temperature or extreme drought. The final opinion part is speculative but novel. It describes an approach to deconstruct resource use efficiencies into their constituent identities or elements based on the Kaya-Porter identity, each of which can be examined for responses to climate and climatic change. We give no promise that the final part is correct’, but we hope it can be a stimulation to thought, hypothesis and experiment, and perhaps a new modelling approach.
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Grosz, B., Dechow, R., Gebbert, S., Hoffmann, H., Zhao, G., Constantin, J., et al. (2017). The implication of input data aggregation on up-scaling soil organic carbon changes. Env. Model. Softw., 96, 361–377.
Abstract: In up-scaling studies, model input data aggregation is a common method to cope with deficient data availability and limit the computational effort. We analyzed model errors due to soil data aggregation for modeled SOC trends. For a region in North West Germany, gridded soil data of spatial resolutions between 1 km and 100 km has been derived by majority selection. This data was used to simulate changes in SOC for a period of 30 years by 7 biogeochemical models. Soil data aggregation strongly affected modeled SOC trends. Prediction errors of simulated SOC changes decreased with increasing spatial resolution of model output. Output data aggregation only marginally reduced differences of model outputs between models indicating that errors caused by deficient model structure are likely to persist even if requirements on the spatial resolution of model outputs are low. (C)2017 Elsevier Ltd. 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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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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