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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Fronzek, S., Pirttioja, N., Carter, T. R., Bindi, M., Hoffmann, H., Palosuo, T., et al. (2018). Classifying multi-model wheat yield impact response surfaces showing sensitivity to temperature and precipitation change. Agric. Syst., 159, 209–224.
Abstract: Crop growth simulation models can differ greatly in their treatment of key processes and hence in their response to environmental conditions. Here, we used an ensemble of 26 process-based wheat models applied at sites across a European transect to compare their sensitivity to changes in temperature (-2 to +9 degrees C) and precipitation (-50 to +50%). Model results were analysed by plotting them as impact response surfaces (IRSs), classifying the IRS patterns of individual model simulations, describing these classes and analysing factors that may explain the major differences in model responses. The model ensemble was used to simulate yields of winter and spring wheat at four sites in Finland, Germany and Spain. Results were plotted as IRSs that show changes in yields relative to the baseline with respect to temperature and precipitation. IRSs of 30-year means and selected extreme years were classified using two approaches describing their pattern. The expert diagnostic approach (EDA) combines two aspects of IRS patterns: location of the maximum yield (nine classes) and strength of the yield response with respect to climate (four classes), resulting in a total of 36 combined classes defined using criteria pre-specified by experts. The statistical diagnostic approach (SDA) groups IRSs by comparing their pattern and magnitude, without attempting to interpret these features. It applies a hierarchical clustering method, grouping response patterns using a distance metric that combines the spatial correlation and Euclidian distance between IRS pairs. The two approaches were used to investigate whether different patterns of yield response could be related to different properties of the crop models, specifically their genealogy, calibration and process description. Although no single model property across a large model ensemble was found to explain the integrated yield response to temperature and precipitation perturbations, the application of the EDA and SDA approaches revealed their capability to distinguish: (i) stronger yield responses to precipitation for winter wheat than spring wheat; (ii) differing strengths of response to climate changes for years with anomalous weather conditions compared to period-average conditions; (iii) the influence of site conditions on yield patterns; (iv) similarities in IRS patterns among models with related genealogy; (v) similarities in IRS patterns for models with simpler process descriptions of root growth and water uptake compared to those with more complex descriptions; and (vi) a closer correspondence of IRS patterns in models using partitioning schemes to represent yield formation than in those using a harvest index. Such results can inform future crop modelling studies that seek to exploit the diversity of multi-model ensembles, by distinguishing ensemble members that span a wide range of responses as well as those that display implausible behaviour or strong mutual similarities.
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Ruiz-Ramos, M., Ferrise, R., Rodriguez, A., Lorite, I. J., Bindi, M., Carter, T. R., et al. (2018). Adaptation response surfaces for managing wheat under perturbed climate and CO2 in a Mediterranean environment. Agric. Syst., 159, 260–274.
Abstract: Adaptation of crops to climate change has to be addressed locally due to the variability of soil, climate and the specific socio-economic settings influencing farm management decisions. Adaptation of rainfed cropping systems in the Mediterranean is especially challenging due to the projected decline in precipitation in the coming decades, which will increase the risk of droughts. Methods that can help explore uncertainties in climate projections and crop modelling, such as impact response surfaces (IRSs) and ensemble modelling, can then be valuable for identifying effective adaptations. Here, an ensemble of 17 crop models was used to simulate a total of 54 adaptation options for rainfed winter wheat (Triticum aestivum) at Lleida (NE Spain). To support the ensemble building, an ex post quality check of model simulations based on several criteria was performed. Those criteria were based on the “According to Our Current Knowledge” (AOCK) concept, which has been formalized here. Adaptations were based on changes in cultivars and management regarding phenology, vernalization, sowing date and irrigation. The effects of adaptation options under changed precipitation (P), temperature (T.),[CO2] and soil type were analysed by constructing response surfaces, which we termed, in accordance with their specific purpose, adaptation response surfaces (ARSs). These were created to assess the effect of adaptations through a range of plausible P, T and [CO2] perturbations. The results indicated that impacts of altered climate were predominantly negative. No single adaptation was capable of overcoming the detrimental effect of the complex interactions imposed by the P, T and [CO2] perturbations except for supplementary irrigation (sI), which reduced the potential impacts under most of the perturbations. Yet, a combination of adaptations for dealing with climate change demonstrated that effective adaptation is possible at Lleida. Combinations based on a cultivar without vernalization requirements showed good and wide adaptation potential. Few combined adaptation options performed well under rainfed conditions. However, a single sI was sufficient to develop a high adaptation potential, including options mainly based on spring wheat, current cycle duration and early sowing date. Depending on local environment (e.g. soil type), many of these adaptations can maintain current yield levels under moderate changes in T and P, and some also under strong changes. We conclude that ARSs can offer a useful tool for supporting planning of field level adaptation under conditions of high uncertainty. (C) 2017 Elsevier Ltd. All rights reserved.
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Pirttioja, N., Carter, T. R., Fronzek, S., Bindi, M., Hoffmann, H., Palosuo, T., et al. (2015). Temperature and precipitation effects on wheat yield across a European transect: a crop model ensemble analysis using impact response surfaces. Clim. Res., 65, 87–105.
Abstract: This study explored the utility of the impact response surface (IRS) approach for investigating model ensemble crop yield responses under a large range of changes in climate. IRSs of spring and winter wheat Triticum aestivum yields were constructed from a 26-member ensemble of process-based crop simulation models for sites in Finland, Germany and Spain across a latitudinal transect. The sensitivity of modelled yield to systematic increments of changes in temperature (-2 to +9°C) and precipitation (-50 to +50%) was tested by modifying values of baseline (1981 to 2010) daily weather, with CO2 concentration fixed at 360 ppm. The IRS approach offers an effective method of portraying model behaviour under changing climate as well as advantages for analysing, comparing and presenting results from multi-model ensemble simulations. Though individual model behaviour occasionally departed markedly from the average, ensemble median responses across sites and crop varieties indicated that yields decline with higher temperatures and decreased precipitation and increase with higher precipitation. Across the uncertainty ranges defined for the IRSs, yields were more sensitive to temperature than precipitation changes at the Finnish site while sensitivities were mixed at the German and Spanish sites. Precipitation effects diminished under higher temperature changes. While the bivariate and multi-model characteristics of the analysis impose some limits to interpretation, the IRS approach nonetheless provides additional insights into sensitivities to inter-model and inter-annual variability. Taken together, these sensitivities may help to pinpoint processes such as heat stress, vernalisation or drought effects requiring refinement in future model development.
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Martre, P., He, J., Le Gouis, J., & Semenov, M. A. (2015). In silico system analysis of physiological traits determining grain yield and protein concentration for wheat as influenced by climate and crop management. J. Experim. Bot., 66(12), 3581–3598.
Abstract: Genetic improvement of grain yield (GY) and grain protein concentration (GPC) is impeded by large genotype×environment×management interactions and by compensatory effects between traits. Here global uncertainty and sensitivity analyses of the process-based wheat model SiriusQuality2 were conducted with the aim of identifying candidate traits to increase GY and GPC. Three contrasted European sites were selected and simulations were performed using long-term weather data and two nitrogen (N) treatments in order to quantify the effect of parameter uncertainty on GY and GPC under variable environments. The overall influence of all 75 plant parameters of SiriusQuality2 was first analysed using the Morris method. Forty-one influential parameters were identified and their individual (first-order) and total effects on the model outputs were investigated using the extended Fourier amplitude sensitivity test. The overall effect of the parameters was dominated by their interactions with other parameters. Under high N supply, a few influential parameters with respect to GY were identified (e.g. radiation use efficiency, potential duration of grain filling, and phyllochron). However, under low N, >10 parameters showed similar effects on GY and GPC. All parameters had opposite effects on GY and GPC, but leaf and stem N storage capacity appeared as good candidate traits to change the intercept of the negative relationship between GY and GPC. This study provides a system analysis of traits determining GY and GPC under variable environments and delivers valuable information to prioritize model development and experimental work.
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