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De Swaef, T., Bellocchi, G., Aper, J., Lootens, P., & Roldan-Ruiz, I. (2019). Use of identifiability analysis in designing phenotyping experiments for modelling forage production and quality. J. Experim. Bot., 70(9), 2587–2604.
Abstract: Agricultural systems models are complex and tend to be over-parameterized with respect to observational datasets. Practical identifiability analysis based on local sensitivity analysis has proved effective in investigating identifiable parameter sets in environmental models, but has not been applied to agricultural systems models. Here, we demonstrate that identifiability analysis improves experimental design to ensure independent parameter estimation for yield and quality outputs of a complex grassland model. The Pasture Simulation model (PaSim) was used to demonstrate the effectiveness of practical identifiability analysis in designing experiments and measurement protocols within phe-notyping experiments with perennial ryegrass. Virtual experiments were designed combining three factors: frequency of measurements, duration of the experiment. and location of trials. Our results demonstrate that (i) PaSim provides sufficient detail in terms of simulating biomass yield and quality of perennial ryegrass for use in breeding, (ii) typical breeding trials are insufficient to parameterize all influential parameters, (iii) the frequency of measurements is more important than the number of growing seasons to improve the identifiability of PaSim parameters, and (iv) identifiability analysis provides a sound approach for optimizing the design of multi-location trials. Practical identifiability analysis can play an important role in ensuring proper exploitation of phenotypic data and cost-effective multi-location experimental designs. Considering the growing importance of simulation models, this study supports the design of experiments and measurement protocols in the phenotyping networks that have recently been organized.
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Castañeda-Vera, A., Leffelaar, P. A., Álvaro-Fuentes, J., Cantero-Martínez, C., & Mínguez, M. I. (2015). Selecting crop models for decision making in wheat insurance. European Journal of Agronomy, 68, 97–116.
Abstract: In crop insurance, the accuracy with which the insurer quantifies the actual risk is highly dependent on the availability on actual yield data. Crop models might be valuable tools to generate data on expected yields for risk assessment when no historical records are available. However, selecting a crop model for a specific objective, location and implementation scale is a difficult task. A look inside the different crop and soil modules to understand how outputs are obtained might facilitate model choice. The objectives of this paper were (i) to assess the usefulness of crop models to be used within a crop insurance analysis and design and (ii) to select the most suitable crop model for drought risk assessment in semi-arid regions in Spain. For that purpose first, a pre-selection of crop models simulating wheat yield under rainfed growing conditions at the field scale was made, and second, four selected models (Aquacrop, CERES-Wheat, CropSyst and WOFOST) were compared in terms of modelling approaches, process descriptions and model outputs. Outputs of the four models for the simulation of winter wheat growth are comparable when water is not limiting, but differences are larger when simulating yields under rainfed conditions. These differences in rainfed yields are mainly related to the dissimilar simulated soil water availability and the assumed linkages with dry matter formation. We concluded that for the simulation of winter wheat growth at field scale in such semi-arid conditions, CERES-Wheat and CropSyst are preferred. WOFOST is a satisfactory compromise between data availability and complexity when detail data on soil is limited. Aquacrop integrates physiological processes in some representative parameters, thus diminishing the number of input parameters, what is seen as an advantage when observed data is scarce. However, the high sensitivity of this model to low water availability limits its use in the region considered. Contrary to the use of ensembles of crop models, we endorse that efforts be concentrated on selecting or rebuilding a model that includes approaches that better describe the agronomic conditions of the regions in which they will be applied. The use of such complex methodologies as crop models is associated with numerous sources of uncertainty, although these models are the best tools available to get insight in these complex agronomic systems. (C) 2015 Elsevier B.V. All rights reserved.
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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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Doltra, J., Olesen, J. E., Báez, D., Louro, A., & Chirinda, N. (2015). Modeling nitrous oxide emissions from organic and conventional cereal-based cropping systems under different management, soil and climate factors. European Journal of Agronomy, 66, 8–20.
Abstract: Mitigation of greenhouse gas emissions from agriculture should be assessed across cropping systems and agroclimatic regions. In this study, we investigate the ability of the FASSET model to analyze differences in the magnitude of N2O emissions due to soil, climate and management factors in cereal-based cropping systems. Forage maize was grown in a conventional dairy system at Mabegondo (NW Spain) and wheat and barley in organic and conventional crop rotations at Foulum (NW Denmark). These two European sites represent agricultural areas with high and low to moderate emission levels, respectively. Field trials included plots with and without catch crops that were fertilized with either mineral N fertilizer, cattle slurry, pig slurry or digested manure. Non-fertilized treatments were also included. Measurements of N2O fluxes during the growing cycle of all the crops at both sites were performed with the static chamber method with more frequent measurements post-fertilization and biweekly measurements when high fluxes were not expected. All cropping systems were simulated with the FASSET version 2.5 simulation model. Cumulative soil seasonal N2O emissions were about ten-fold higher at Mabegondo than at Foulum when averaged across systems and treatments (8.99 and 0.71 kg N2O-N ha(-1), respectively). The average simulated cumulative soil N2O emissions were 9.03 and 1.71 kg N2O-N ha(-1) at Mabegondo and at Foulum, respectively. Fertilization, catch crops and cropping systems had lower influence on the seasonal soil N2O fluxes than the environmental factors. Overall, in its current version FASSET reproduced the effects of the different factors investigated on the cumulative seasonal soil N2O emissions but temporally it overestimated emissions from nitrification and denitrification on particular days when soil operations, ploughing or fertilization, took place. The errors associated with simulated daily soil N2O fluxes increased with the magnitude of the emissions. For resolving causes of differences in simulated and measured fluxes more intensive and temporally detailed measurements of N2O fluxes and soil C and N dynamics would be needed. (C) 2015 Elsevier B.V. All rights reserved.
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Ramirez-Villegas, J., Watson, J., & Challinor, A. J. (2015). Identifying traits for genotypic adaptation using crop models. J. Experim. Bot., 66(12), 3451–3462.
Abstract: Genotypic adaptation involves the incorporation of novel traits in crop varieties so as to enhance food productivity and stability and is expected to be one of the most important adaptation strategies to future climate change. Simulation modelling can provide the basis for evaluating the biophysical potential of crop traits for genotypic adaptation. This review focuses on the use of models for assessing the potential benefits of genotypic adaptation as a response strategy to projected climate change impacts. Some key crop responses to the environment, as well as the role of models and model ensembles for assessing impacts and adaptation, are first reviewed. Next, the review describes crop-climate models can help focus the development of future-adapted crop germplasm in breeding programmes. While recently published modelling studies have demonstrated the potential of genotypic adaptation strategies and ideotype design, it is argued that, for model-based studies of genotypic adaptation to be used in crop breeding, it is critical that modelled traits are better grounded in genetic and physiological knowledge. To this aim, two main goals need to be pursued in future studies: (i) a better understanding of plant processes that limit productivity under future climate change; and (ii) a coupling between genetic and crop growth models-perhaps at the expense of the number of traits analysed. Importantly, the latter may imply additional complexity (and likely uncertainty) in crop modelling studies. Hence, appropriately constraining processes and parameters in models and a shift from simply quantifying uncertainty to actually quantifying robustness towards modelling choices are two key aspects that need to be included into future crop model-based analyses of genotypic adaptation.
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