| Records |
| Author |
Van Oijen, M.; Höglind, M. |
Title  |
Toward a Bayesian procedure for using process-based models in plant breeding, with application to ideotype design |
Type |
Journal Article |
| Year |
2016 |
Publication |
Euphytica |
Abbreviated Journal |
Euphytica |
| Volume |
207 |
Issue |
3 |
Pages |
627-643 |
| 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 |
| 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. |
| Address |
2016-10-31 |
| Corporate Author |
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Thesis |
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Place of Publication |
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| Language |
English |
Summary Language |
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Original Title |
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Series Title |
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Series Issue |
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Edition |
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| ISSN |
0014-2336 |
ISBN |
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Article |
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Conference |
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| Notes |
CropM, ft_macsur |
Approved |
no |
| Call Number |
MA @ admin @ |
Serial |
4820 |
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| Author |
Jing, Q.; Bélanger, G.; Baron, V.; Bonesmo, H.; Virkajärvi, P. |
| Title |
Simulating the Nutritive Value of Timothy Summer Regrowth |
Type |
Journal Article |
| Year |
2013 |
Publication |
Agronomy Journal |
Abbreviated Journal |
Agronomy Journal |
| Volume |
105 |
Issue |
3 |
Pages |
563 |
| Keywords |
varying n nutrition; cation-anion difference; spring growth; swine manure; leaf-area; nitrogen; yield; model; digestibility; dynamics |
| 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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Place of Publication |
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| Language |
English |
Summary Language |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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| ISSN |
0002-1962 |
ISBN |
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Article |
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Conference |
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| Notes |
CropM, LiveM |
Approved |
no |
| Call Number |
MA @ admin @ |
Serial |
4493 |
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| Author |
De Pascale, S.; Orsini, F.; Caputo, R.; Palermo, M.A.; Barbieri, G.; Maggio, A. |
| Title |
Seasonal and multiannual effects of salinisation on tomato yield and fruit quality |
Type |
Journal Article |
| Year |
2012 |
Publication |
Functional Plant Biology |
Abbreviated Journal |
Functional Plant Biology |
| Volume |
39 |
Issue |
8 |
Pages |
689-698 |
| Keywords |
fruit ions concentration; fruit lipophilic and hydrophilic antioxidant; capacities; leaf water potentials; leaf stomatal conductance; short- and; long-term salinisation; salinity tolerance; water-stress; antioxidant activity; irrigation; growth; plants; soils; carotenoids; responses; crops |
| Abstract |
The effects of short-and long-term salinisation were studied by comparing tomato growth on a soil exposed to one-season salinisation (short term) vs growth on a soil exposed to >20 years salinisation (long term). Remarkable differences were associated to substantial modifications of the soil physical-chemical characteristics in the root zone, including deteriorated structure, reduced infiltration properties and increased pH. Fresh yield, fruit number and fruit weight were similarly affected by short-and long-term salinisation. In contrast, the marketable yield was significantly lower in the long-term salinised soil-a response that was also associated to nutritional imbalance (mainly referred to P and K). As reported for plants growing under oxygen deprivation stress, the antioxidant capacity of the water soluble fraction of salinised tomato fruits was enhanced by short-term salinisation, also. Overall, long-term salinisation may cause physiological imbalances and yield reductions that cannot be solely attributed to hyperosmotic stress and ionic toxicity. Therefore, the ability of plants to cope with nutritional deficiency and withstand high pH and anoxia may be important traits that should be considered to improve plant tolerance to long-term salinised soils. |
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| Language |
English |
Summary Language |
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Original Title |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
1445-4408 |
ISBN |
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Article |
| Area |
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Expedition |
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Conference |
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| Notes |
CropM |
Approved |
no |
| Call Number |
MA @ admin @ |
Serial |
4583 |
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| Author |
Jing, Q.; Bélanger, G.; Baron, V.; Bonesmo, H.; Virkajärvi, P.; Young, D. |
| Title |
Regrowth simulation of the perennial grass timothy |
Type |
Journal Article |
| Year |
2012 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
| Volume |
232 |
Issue |
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Pages |
64-77 |
| 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 |
| 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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English |
Summary Language |
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Original Title |
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Series Title |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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| ISSN |
0304-3800 |
ISBN |
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Medium |
Article |
| Area |
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Expedition |
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Conference |
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| Notes |
CropM, LiveM |
Approved |
no |
| Call Number |
MA @ admin @ |
Serial |
4473 |
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| Author |
Mansouri, M.; Dumont, B.; Destain, M.-F. |
| Title |
Modeling and prediction of nonlinear environmental system using Bayesian methods |
Type |
Journal Article |
| Year |
2013 |
Publication |
Computers and Electronics in Agriculture |
Abbreviated Journal |
Computers and Electronics in Agriculture |
| Volume |
92 |
Issue |
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Pages |
16-31 |
| Keywords |
state and parameter estimation; variational filter; particle filter; extended kalman filter; nonlinear environmental system; leaf area index and soil moisture model; extended kalman filter; state-space models; parameter-estimation; particle filters; navigation; tutorial; tracking |
| Abstract |
An environmental dynamic system is usually modeled as a nonlinear system described by a set of nonlinear ODEs. A central challenge in computational modeling of environmental systems is the determination of the model parameters. In these cases, estimating these variables or parameters from other easily obtained measurements can be extremely useful. This work addresses the problem of monitoring and modeling a leaf area index and soil moisture model (LSM) using state estimation. The performances of various conventional and state-of-the-art state estimation techniques are compared when they are utilized to achieve this objective. These techniques include the extended Kalman filter (EKF), particle filter (PF), and the more recently developed technique variational filter (VF). Specifically, two comparative studies are performed. In the first comparative study, the state variables (the leaf-area index LAI, the volumetric water content of the soil layer 1, HUR1 and the volumetric water content of the soil layer 2, HUR2) are estimated from noisy measurements of these variables, and the various estimation techniques are compared by computing the estimation root mean square error (RMSE) with respect to the noise-free data. In the second comparative study, the state variables as well as the model parameters are simultaneously estimated. In this case, in addition to comparing the performances of the various state estimation techniques, the effect of number of estimated model parameters on the accuracy and convergence of these techniques are also assessed. The results of both comparative studies show that the PF provides a higher accuracy than the EKF, which is due to the limited ability of the EKF to handle highly nonlinear processes. The results also show that the VF provides a significant improvement over the PF because, unlike the PF which depends on the choice of sampling distribution used to estimate the posterior distribution, the VF yields an optimum choice of the sampling distribution, which also accounts for the observed data. The results of the second comparative study show that, for all techniques, estimating more model parameters affects the estimation accuracy as well as the convergence of the estimated states and parameters. However, the VF can still provide both convergence as well as accuracy related advantages over other estimation methods. (C) 2013 Elsevier B.V. All rights reserved. |
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Place of Publication |
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English |
Summary Language |
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Original Title |
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Series Title |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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| ISSN |
0168-1699 |
ISBN |
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Article |
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Expedition |
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| Notes |
CropM |
Approved |
no |
| Call Number |
MA @ admin @ |
Serial |
4495 |
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