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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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Mansouri, M., Dumont, B., Leemans, V., & Destain, M. - F. (2014). Bayesian methods for predicting LAI and soil water content. Precision Agric., 15(2), 184–201.
Abstract: LAI of winter wheat (Triticum aestivum L.) and soil water content of the topsoil (200 mm) and of the subsoil (500 mm) were considered as state variables of a dynamic soil-crop system. This system was assumed to progress according to a Bayesian probabilistic state space model, in which real values of LAI and soil water content were daily introduced in order to correct the model trajectory and reach better future evolution. The chosen crop model was mini STICS which can reduce the computing and execution times while ensuring the robustness of data processing and estimation. To predict simultaneously state variables and model parameters in this non-linear environment, three techniques were used: extended Kalman filtering (EKF), particle filtering (PF), and variational filtering (VF). The significantly improved performance of the VF method when compared to EKF and PF is demonstrated. The variational filter has a low computational complexity and the convergence speed of states and parameters estimation can be adjusted independently. Detailed case studies demonstrated that the root mean square error of the three estimated states (LAI and soil water content of two soil layers) was smaller and that the convergence of all considered parameters was ensured when using VF. Assimilating measurements in a crop model allows accurate prediction of LAI and soil water content at a local scale. As these biophysical properties are key parameters in the crop-plant system characterization, the system has the potential to be used in precision farming to aid farmers and decision makers in developing strategies for site-specific management of inputs, such as fertilizers and water irrigation.
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Angulo, C., Rötter, R., Lock, R., Enders, A., Fronzek, S., & Ewert, F. (2013). Implication of crop model calibration strategies for assessing regional impacts of climate change in Europe. Agricultural and Forest Meteorology, 170, 32–46.
Abstract: Process-based crop simulation models are increasingly used in regional climate change impact studies, but little is known about the implications of different calibration strategies on simulated yields. This study aims to assess the importance of region-specific calibration of five important field crops (winter wheat, winter barley, potato, sugar beet and maize) across 25 member countries of the European Union (EU25). We examine three calibration strategies and their implications on spatial and temporal yield variability in response to climate change: (i) calculation of phenology parameters only, (ii) consideration of both phenology calibration and a yield correction factor and (iii) calibration of phenology and selected growth processes. The analysis is conducted for 533 climate zones, considering 24 years of observed yield data (1983-2006). The best performing strategy is used to estimate the impacts of climate change, increasing CO2 concentration and technology development on yields for the five crops across EU25, using seven climate change scenarios for the period 2041-2064. Simulations and calibrations are performed with the crop model LINTUL2 combined with a calibration routine implemented in the modelling interface LINTUL-FAST. The results show that yield simulations improve if growth parameters are considered in the calibration for individual regions (strategy 3); e.g. RMSE values for simulated winter wheat yield are 2.36, 1.10 and 0.70 Mg ha(-1) for calibration strategies 1, 2 and 3, respectively. The calibration strategy did not only affect the model simulations under reference climate but also the extent of the simulated climate change impacts. Applying the calibrated model for impact assessment revealed that climatic change alone will reduce crop yields. Consideration of the effects of increasing CO2 concentration and technology development resulted in yield increases for all crops except maize (i.e. the negative effects of climate change were outbalanced by the positive effects of CO2 and technology change), with considerable differences between scenarios and regions. Our simulations also suggest some increase in yield variability due to climate change which, however, is less pronounced than the differences among scenarios which are particularly large when the effects of CO2 concentration and technology development are considered. Our results stress the need for region-specific calibration of crop models used for Europe-wide assessments. Limitations of the considered strategies are discussed. We recommend that future work should focus on obtaining more comprehensive, high quality data with a finer resolution allowing application of improved strategies for model calibration that better account for spatial differences and changes over time in the growth and development parameters used in crop models. (c) 2012 Elsevier B.V. All rights reserved.
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Bernabucci, U., Biffani, S., Buggiotti, L., Vitali, A., Lacetera, N., & Nardone, A. (2014). The effects of heat stress in Italian Holstein dairy cattle. J. Dairy Sci., 97(1), 471–486.
Abstract: The data set for this study comprised 1,488,474 test-day records for milk, fat, and protein yields and fat and protein percentages from 191,012 first-, second-, and third-parity Holstein cows from 484 farms. Data were collected from 2001 through 2007 and merged with meteorological data from 35 weather stations. A linear model (M1) was used to estimate the effects of the temperature-humidity index (THI) on production traits. Least squares means from M1 were used to detect the THI thresholds for milk production in all parities by using a 2-phase linear regression procedure (M2). A multiple-trait repeatability test-model (M3) was used to estimate variance components for all traits and a dummy regression variable (t) was defined to estimate the production decline caused by heat stress. Additionally, the estimated variance components and M3 were used to estimate traditional and heat-tolerance breeding values (estimated breeding values, EBV) for milk yield and protein percentages at parity 1. An analysis of data (M2) indicated that the daily THI at which milk production started to decline for the 3 parities and traits ranged from 65 to 76. These THI values can be achieved with different temperature/humidity combinations with a range of temperatures from 21 to 36°C and relative humidity values from 5 to 95%. The highest negative effect of THI was observed 4 d before test day over the 3 parities for all traits. The negative effect of THI on production traits indicates that first-parity cows are less sensitive to heat stress than multiparous cows. Over the parities, the general additive genetic variance decreased for protein content and increased for milk yield and fat and protein yield. Additive genetic variance for heat tolerance showed an increase from the first to third parity for milk, protein, and fat yield, and for protein percentage. Genetic correlations between general and heat stress effects were all unfavorable (from -0.24 to -0.56). Three EBV per trait were calculated for each cow and bull (traditional EBV, traditional EBV estimated with the inclusion of THI covariate effect, and heat tolerance EBV) and the rankings of EBV for 283 bulls born after 1985 with at least 50 daughters were compared. When THI was included in the model, the ranking for 17 and 32 bulls changed for milk yield and protein percentage, respectively. The heat tolerance genetic component is not negligible, suggesting that heat tolerance selection should be included in the selection objectives.
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Lorite, I. J., García-Vila, M., Santos, C., Ruiz-Ramos, M., & Fereres, E. (2013). AquaData and AquaGIS: Two computer utilities for temporal and spatial simulations of water-limited yield with AquaCrop. Computers and Electronics in Agriculture, 96, 227–237.
Abstract: The crop simulation model AquaCrop, recently developed by FAO can be used for a wide range of purposes. However, in its present form, its use over large areas or for applications that require a large number of simulations runs (e.g., long-term analysis), is not practical without developing software to facilitate such applications. Two tools for managing the inputs and outputs of AquaCrop, named AquaData and AquaGIS, have been developed for this purpose and are presented here. Both software utilities have been programmed in Delphi v. 5 and in addition, AquaGIS requires the Geographic Information System (GIS) programming tool MapObjects. These utilities allow the efficient management of input and output files, along with a GIS module to develop spatial analysis and effect spatial visualization of the results, facilitating knowledge dissemination. A sample of application of the utilities is given here, as an AquaCrop simulation analysis of impact of climate change on wheat yield in Southern Spain, which requires extensive input data preparation and output processing. The use of AquaCrop without the two utilities would have required approximately 1000 h of work, while the utilization of AquaData and AquaGIS reduced that time by more than 99%. Furthermore, the use of GIS, made it possible to perform a spatial analysis of the results, thus providing a new option to extend the use of the AquaCrop model to scales requiring spatial and temporal analyses. (C) 2013 Elsevier B.V. All rights reserved.
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