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Van Oijen, M., & Höglind, M. (2016). Toward a Bayesian procedure for using process-based models in plant breeding, with application to ideotype design. Euphytica, 207(3), 627–643.
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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Semenov, M. A., Stratonovitch, P., Alghabari, F., & Gooding, M. J. (2014). Adapting wheat in Europe for climate change. J. Ceareal Sci., 59(3), 245–256.
Abstract: Increasing cereal yield is needed to meet the projected increased demand for world food supply of about 70% by 2050. Sirius, a process-based model for wheat, was used to estimate yield potential for wheat ideotypes optimized for future climatic projections for ten wheat growing areas of Europe. It was predicted that the detrimental effect of drought stress on yield would be decreased due to enhanced tailoring of phenology to future weather patterns, and due to genetic improvements in the response of photosynthesis and green leaf duration to water shortage. Yield advances could be made through extending maturation and thereby improve resource capture and partitioning. However the model predicted an increase in frequency of heat stress at meiosis and anthesis. Controlled environment experiments quantify the effects of heat and drought at booting and flowering on grain numbers and potential grain size. A current adaptation of wheat to areas of Europe with hotter and drier summers is a quicker maturation which helps to escape from excessive stress, but results in lower yields. To increase yield potential and to respond to climate change, increased tolerance to heat and drought stress should remain priorities for the genetic improvement of wheat.
Keywords: A, maximum area of flag leaf area; ABA, abscisic acid; CV, coefficient of variation; Crop improvement; Crop modelling; FC, field capacity; GMT, Greenwich mean time; GS, growth stage; Gf, grain filling duration; HI, harvest index; HSP, heat shock protein; Heat and drought tolerance; Impact assessment; LAI, leaf area index; Ph, phylochron; Pp, photoperiod response; Ru, root water uptake; S, duration of leaf senescence; SF, drought stress factor; Sirius; Wheat ideotype
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Orsini, F., Alnayef, M., Bona, S., Maggio, A., & Gianquinto, G. (2012). Low stomatal density and reduced transpiration facilitate strawberry adaptation to salinity. Environmental and Experimental Botany, 81, 1–10.
Abstract: Water and soil salinization are major constraints to agricultural productions because plant adaptation to hyperosmotic environments is generally associated to reduced growth and ultimately yield loss. Understanding the physiological/molecular mechanisms that link adaptation and growth is one of the greatest challenges in plant stress research since it would allow us to better define strategies to improve crop salt tolerance. In this study we attempted to establish a functional link between morphological and physiological traits in strawberry in order to identify margins to “uncouple” plant growth and stress adaptation. Two strawberry cultivars, Elsanta and Elsinore, were grown under 0, 10.20 and 40 mM NaCl. Upon salinization Elsanta plants maintained a larger and more functional leaf area compared to Elsinore plants, which were irreversibly damaged at 40 mM NaCl. The tolerance of Elsanta was correlated with a constitutive reduced transpirational flux due to low stomata! density (173 vs. 234 stomata mm(-2) in Elsanta and Elsinore, respectively), which turned out to be critical to pre-adapt plants to the oncoming stress. The reduced transpiration rate of Elsanta (14.7 g H2O plant(-1) h(-1)) respect to Elsinore (17.7 g H2O plant(-1) h(-1)) most likely delayed the accumulation of toxic ions into the leaves, preserved tissues dehydration and consented to adjust more effectively to the hyperosmotic environment. Although we cannot rule out the contribution of other physiological and molecular mechanisms to the relatively higher tolerance of Elsanta, here we demonstrate that low stomatal density may be beneficial for cultivars prescribed to be used in marginal environments in terms of salinity and/or drought. (C) 2012 Elsevier B.V. All rights reserved.
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Minet, J., Laloy, E., Tychon, B., & François, L. (2015). Bayesian inversions of a dynamic vegetation model at four European grassland sites. Biogeosciences, 12(9), 2809–2829.
Abstract: 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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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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