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Author  |
Jing, Q.; Bélanger, G.; Baron, V.; Bonesmo, H.; Virkajärvi, P. |
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Title |
Simulating the Nutritive Value of Timothy Summer Regrowth |
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Journal Article |
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Year |
2013 |
Publication |
Agronomy Journal |
Abbreviated Journal |
Agronomy Journal |
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Volume |
105 |
Issue |
3 |
Pages |
563 |
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Keywords |
varying n nutrition; cation-anion difference; spring growth; swine manure; leaf-area; nitrogen; yield; model; digestibility; dynamics |
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Abstract |
The process-based grass model, CATIMO, simulates the spring growth and nutritive value of timothy (Phleum pratense L.), a forage species widely grown in Scandinavia and Canada, but the nutritive value of the summer regrowth has never been simulated. Our objective was to improve CATIMO for simulating the N concentration, neutral detergent fiber (NDF), in vitro digestibility of NDF (dNDF), and in vitro true digestibility of dry matter (IVTD) of summer regrowth. Daily changes in summer regrowth nutritive value were simulated by modifying key crop parameters that differed from spring growth. More specifically, the partitioning fraction to leaf blades was increased to increase the leaf-to-weight ratio, and daily changes in NDF and dNDF of leaf blades and stems were reduced. The modified CATIMO model was evaluated with data from four independent experiments in eastern and western Canada and Finland. The model performed better for eastern Canada than for the other locations, but the nutritive value attributes of the summer regrowth across locations (range of normalized RMSE = 8-25%, slope < 0.17, R-2 < 0.10) were not simulated as well as those of the spring growth (range of normalized RMSE = 4-16%, 0.85 < slope < 1.07, R-2 > 0.61). These modeling results highlight knowledge gaps in timothy summer regrowth and prospective research directions: improved knowledge of factors controlling the nutritive value of the timothy summer regrowth and experimental measurements of leaf-to-weight ratio and of the nutritive value of leaves and stems. |
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0002-1962 |
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CropM, LiveM |
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MA @ admin @ |
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4493 |
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Author |
Jing, Q.; Bélanger, G.; Baron, V.; Bonesmo, H.; Virkajärvi, P.; Young, D. |
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Title |
Regrowth simulation of the perennial grass timothy |
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Journal Article |
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Year |
2012 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
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Volume |
232 |
Issue |
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Pages |
64-77 |
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Keywords |
biomass; carbohydrate; leaf area index; n uptake; reserve-dependent growth; temperature; nutritive-value; carbohydrate reserves; phleum-pratense; catimo model; leaf-area; nitrogen-fertilization; spring harvest; meadow fescue; tall fescue; growth |
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Abstract |
Several process-based models for simulating the growth of perennial grasses have been developed but few include the simulation of regrowth. The model CATIMO simulates the primary growth of timothy (Phleum pratense L), an important perennial forage grass species in northern regions of Europe and North America. Our objective was to further develop the model CATIMO to simulate timothy regrowth using the concept of reserve-dependent growth. The performance of this modified CATIMO model in simulating leaf area index (LAI), biomass dry matter (DM) yield, and N uptake of regrowth was assessed with data from four independent field experiments in Norway, Finland, and western and eastern Canada using an approach that combines graphical comparison and statistical analysis. Biomass DM yield and N uptake of regrowth were predicted at the same accuracy as primary growth with linear regression coefficients of determination between measured and simulated values greater than 0.79, model simulation efficiencies greater than 0.78, and normalized root mean square errors (14-30% for biomass and 24-34% for N uptake) comparable with the coefficients of variation of measured data (1-21% for biomass and 1-25% for N uptake). The model satisfactorily simulated the regrowth LAI but only up to a value of about 4.0. The modified CATIMO model with its capacity to simulate regrowth provides a framework to simulate perennial grasses with multiple harvests, and to explore management options for sustainable grass production under different environmental conditions. Crown Copyright (C) 2012 Published by Elsevier B.V. All rights reserved. |
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0304-3800 |
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CropM, LiveM |
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MA @ admin @ |
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4473 |
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Author |
Mansouri, M.; Dumont, B.; Leemans, V.; Destain, M.-F. |
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Title |
Bayesian methods for predicting LAI and soil water content |
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Journal Article |
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Year |
2014 |
Publication |
Precision Agriculture |
Abbreviated Journal |
Precision Agric. |
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15 |
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2 |
Pages |
184-201 |
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Keywords |
crop model; bayes; data assimilation; extended kalman filtering; particle filtering; variational filtering; leaf-area index; parameter-estimation; crop models; moisture; instruments; management; sensors; state |
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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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1385-2256 |
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CropM, ftnotmacsur |
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MA @ admin @ |
Serial |
4629 |
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Minet, J.; Laloy, E.; Tychon, B.; François, L. |
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Title |
Bayesian inversions of a dynamic vegetation model at four European grassland sites |
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Journal Article |
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2015 |
Publication |
Biogeosciences |
Abbreviated Journal |
Biogeosciences |
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12 |
Issue |
9 |
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2809-2829 |
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Keywords |
eddy-covariance data; terrestrial ecosystem model; bioclimatic affinity; groups; monte-carlo-simulation; dry-matter content; leaf-area; climate-change; stomatal conductance; parameter-estimation; plant |
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Eddy covariance data from four European grassland sites are used to probabilistically invert the CARAIB (CARbon Assimilation In the Biosphere) dynamic vegetation model (DVM) with 10 unknown parameters, using the DREAM((ZS)) (DiffeRential Evolution Adaptive Metropolis) Markov chain Monte Carlo (MCMC) sampler. We focus on comparing model inversions, considering both homoscedastic and heteroscedastic eddy covariance residual errors, with variances either fixed a priori or jointly inferred together with the model parameters. Agreements between measured and simulated data during calibration are comparable with previous studies, with root mean square errors (RMSEs) of simulated daily gross primary productivity (GPP), ecosystem respiration (RECO) and evapotranspiration (ET) ranging from 1.73 to 2.19, 1.04 to 1.56 g C m(-2) day(-1) and 0.50 to 1.28 mm day(-1), respectively. For the calibration period, using a homoscedastic eddy covariance residual error model resulted in a better agreement between measured and modelled data than using a heteroscedastic residual error model. However, a model validation experiment showed that CARAIB models calibrated considering heteroscedastic residual errors perform better. Posterior parameter distributions derived from using a heteroscedastic model of the residuals thus appear to be more robust. This is the case even though the classical linear heteroscedastic error model assumed herein did not fully remove heteroscedasticity of the GPP residuals. Despite the fact that the calibrated model is generally capable of fitting the data within measurement errors, systematic bias in the model simulations are observed. These are likely due to model inadequacies such as shortcomings in the photosynthesis modelling. Besides the residual error treatment, differences between model parameter posterior distributions among the four grassland sites are also investigated. It is shown that the marginal distributions of the specific leaf area and characteristic mortality time parameters can be explained by site-specific ecophysiological characteristics. |
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1726-4189 |
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CropM LiveM, ft_macsur |
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MA @ admin @ |
Serial |
4571 |
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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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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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MA @ admin @ |
Serial |
4820 |
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