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Author |
Van Oijen, M.; Höglind, M. |
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Title |
Toward a Bayesian procedure for using process-based models in plant breeding, with application to ideotype design |
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Journal Article |
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Year |
2016 |
Publication |
Euphytica |
Abbreviated Journal |
Euphytica |
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Volume |
207 |
Issue |
3 |
Pages |
627-643 |
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Keywords |
BASGRA; cold tolerance; genotype-environment interaction; plant breeding; process-based modelling; yield stability; grassland productivity; timothy regrowth; climate-change; water-deficit; forest models; late blight; leaf-area; calibration; growth; tolerance |
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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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2016-10-31 |
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0014-2336 |
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CropM, ft_macsur |
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Call Number |
MA @ admin @ |
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4820 |
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Author |
Höglind, M.; Van Oijen, M.; Cameron, D.; Persson, T. |
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Title |
Process-based simulation of growth and overwintering of grassland using the BASGRA model |
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Journal Article |
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Year |
2016 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
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Volume |
335 |
Issue |
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Pages |
1-15 |
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Keywords |
Cold hardening; Frost injury; Phleum pratense L.; Process-based; modelling; Winter survival; Yield; low-temperature tolerance; perennial forage crops; dry-matter; production; climate-change; nutritive-value; snow-cover; bayesian; calibration; timothy regrowth; phleum-pratense; lolium-perenne |
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Abstract |
Process-based models (PBM) for simulation of weather dependent grass growth can assist farmers and plant breeders in addressing the challenges of climate change by simulating alternative roads of adaptation. They can also provide management decision support under current conditions. A drawback of existing grass models is that they do not take into account the effect of winter stresses, limiting their use for full-year simulations in areas where winter survival is a key factor for yield security. Here, we present a novel full-year PBM for grassland named BASGRA. It was developed by combining the LINGRA grassland model (Van Oijen et al., 2005a) with models for cold hardening and soil physical winter processes. We present the model and show how it was parameterized for timothy (Phleum pratense L.), the most important forage grass in Scandinavia and parts of North America and Asia. Uniquely, BASGRA simulates the processes taking place in the sward during the transition from summer to winter, including growth cessation and gradual cold hardening, and functions for simulating plant injury due to low temperatures, snow and ice affecting regrowth in spring. For the calibration, we used detailed data from five different locations in Norway, covering a wide range of agroclimatic regions, day lengths (latitudes from 59 degrees to 70 degrees N) and soil conditions. The total dataset included 11 variables, notably above-ground dry matter, leaf area index, tiller density, content of C reserves, and frost tolerance. All data were used in the calibration. When BASGRA was run with the maximum a-posteriori (MAP) parameter vector from the single, Bayesian calibration, nearly all measured variables were simulated to an overall normalized root mean squared error (NRMSE) <0.5. For many site x experiment combinations, NRMSE was <0.3. The temporal dynamics were captured well for most variables, as evaluated by comparing simulated time courses versus data for the individual sites. The results may suggest that BASGRA is a reasonably robust model, allowing for simulation of growth and several important underlying processes with acceptable accuracy for a range of agroclimatic conditions. However, the robustness of the model needs to be tested further using independent data from a wide range of growing conditions. Finally we show an example of application of the model, comparing overwintering risks in two climatically different sites, and discuss future model applications. Further development work should include improved simulation of the dynamics of C reserves, and validation of winter tiller dynamics against independent data. (C) 2016 Elsevier B.V. All rights reserved. |
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2016-07-28 |
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0304-3800 |
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CropM, LiveM, ft_macsur |
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MA @ admin @ |
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4764 |
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Author |
Balkovič, J.; van der Velde, M.; Schmid, E.; Skalský, R.; Khabarov, N.; Obersteiner, M.; Stürmer, B.; Xiong, W. |
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Title |
Pan-European crop modelling with EPIC: Implementation, up-scaling and regional crop yield validation |
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Journal Article |
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2013 |
Publication |
Agricultural Systems |
Abbreviated Journal |
Agricultural Systems |
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120 |
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61-75 |
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Keywords |
EPIC; large-scale crop modelling; model performance testing; EU; climate-change; high-resolution; organic-carbon; growth-model; wheat yield; water; calibration; impacts; productivity; simulations |
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Justifiable usage of large-scale crop model simulations requires transparent, comprehensive and spatially extensive evaluations of their performance and associated accuracy. Simulated crop yields of a Pan-European implementation of the Environmental Policy Integrated Climate (EPIC) crop model were satisfactorily evaluated with reported regional yield data from EUROSTAT for four major crops, including winter wheat, rainfed and irrigated maize, spring barley and winter rye. European-wide land use, elevation, soil and daily meteorological gridded data were integrated in GIS and coupled with EPIC. Default EPIC crop and biophysical process parameter values were used with some minor adjustments according to suggestions from scientific literature. The model performance was improved by spatial calculations of crop sowing densities, potential heat units, operation schedules, and nutrient application rates. EPIC performed reasonable in the simulation of regional crop yields, with long-term averages predicted better than inter-annual variability: linear regression R-2 ranged from 0.58 (maize) to 0.91 (spring barley) and relative estimation errors were between +/- 30% for most of the European regions. The modelled and reported crop yields demonstrated similar responses to driving meteorological variables. However, EPIC performed better in dry compared to wet years. A yield sensitivity analysis of crop nutrient and irrigation management factors and cultivar specific characteristics for contrasting regions in Europe revealed a range in model response and attainable yields. We also show that modelled crop yield is strongly dependent on the chosen PET method. The simulated crop yield variability was lower compared to reported crop yields. This assessment should contribute to the availability of harmonised and transparently evaluated agricultural modelling tools in the EU as well as the establishment of modelling benchmarks as a requirement for sound and ongoing policy evaluations in the agricultural and environmental domains. (C) 2013 The Authors. Published by Elsevier Ltd. All rights reserved. |
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2016-06-01 |
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0308-521x |
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CropM, ft_macsur |
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MA @ admin @ |
Serial |
4737 |
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Author |
Webber, H.; Zhao, G.; Wolf, J.; Britz, W.; Vries, W. de; Gaiser, T.; Hoffmann, H.; Ewert, F. |
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Title |
Climate change impacts on European crop yields: Do we need to consider nitrogen limitation |
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Journal Article |
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Year |
2015 |
Publication |
European Journal of Agronomy |
Abbreviated Journal |
European Journal of Agronomy |
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71 |
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123-134 |
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Keywords |
Climate impact assessment; Nitrogen limitation; European crop yields; SIMPLACE Crop modelling framework; model calibration; winter-wheat; scale; co2; productivity; agriculture; strategies; scenarios; systems; growth |
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Global climate impact studies with crop models suggest that including nitrogen and water limitation causes greater negative climate change impacts on actual yields compared to water-limitation only. We simulated water limited and nitrogen water limited yields across the EU-27 to 2050 for six key crops with the SIMPLACE<LINTUL5, DRUNIR, HEAT> model to assess how important consideration of nitrogen limitation is in climate impact studies for European cropping systems. We further investigated how crop nitrogen use may change under future climate change scenarios. Our results suggest that inclusion of nitrogen limitation hardly changed crop yield response to climate for the spring-sown crops considered (grain maize, potato, and sugar beet). However, for winter-sown crops (winter barley, winter rapeseed and winter wheat), simulated impacts to 2050 were more negative when nitrogen limitation was considered, especially with high levels of water stress. Future nitrogen use rates are likely to decrease due to climate change for spring-sown crops, largely in parallel with their yields. These results imply that climate change impact studies for winter-sown crops should consider N-fertilization. Specification of future N fertilization rates is a methodological challenge that is likely to need integrated assessment models to address. |
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1161-0301 |
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CropM, ft_macsur |
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MA @ admin @ |
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4726 |
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Hoffmann, H.; Zhao, G.; Asseng, S.; Bindi, M.; Biernath, C.; Constantin, J.; Coucheney, E.; Dechow, R.; Doro, L.; Eckersten, H.; Gaiser, T.; Grosz, B.; Heinlein, F.; Kassie, B.T.; Kersebaum, K.-C.; Klein, C.; Kuhnert, M.; Lewan, E.; Moriondo, M.; Nendel, C.; Priesack, E.; Raynal, H.; Roggero, P.P.; Rötter, R.P.; Siebert, S.; Specka, X.; Tao, F.; Teixeira, E.; Trombi, G.; Wallach, D.; Weihermüller, L.; Yeluripati, J.; Ewert, F. |
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Title |
Impact of spatial soil and climate input data aggregation on regional yield simulations |
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Journal Article |
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Year |
2016 |
Publication |
PLoS One |
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PLoS One |
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Volume |
11 |
Issue |
4 |
Pages |
e0151782 |
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Keywords |
systems simulation; nitrogen dynamics; winter-wheat; crop models; data resolution; scale; water; variability; calibration; weather |
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We show the error in water-limited yields simulated by crop models which is associated with spatially aggregated soil and climate input data. Crop simulations at large scales (regional, national, continental) frequently use input data of low resolution. Therefore, climate and soil data are often generated via averaging and sampling by area majority. This may bias simulated yields at large scales, varying largely across models. Thus, we evaluated the error associated with spatially aggregated soil and climate data for 14 crop models. Yields of winter wheat and silage maize were simulated under water-limited production conditions. We calculated this error from crop yields simulated at spatial resolutions from 1 to 100 km for the state of North Rhine-Westphalia, Germany. Most models showed yields biased by <15% when aggregating only soil data. The relative mean absolute error (rMAE) of most models using aggregated soil data was in the range or larger than the inter-annual or inter-model variability in yields. This error increased further when both climate and soil data were aggregated. Distinct error patterns indicate that the rMAE may be estimated from few soil variables. Illustrating the range of these aggregation effects across models, this study is a first step towards an ex-ante assessment of aggregation errors in large-scale simulations. |
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1932-6203 |
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CropM, ft_macsur |
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MA @ admin @ |
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4725 |
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