A conceptual framework for the dynamic modeling of time-resolved phenotypes for sets of genotype-environment-management combinations: a model library.

Introduction: Dynamic crop growth models are an important tool to predict complex traits, like crop yield, for modern and future genotypes in their current and evolving environments, as those occurring under climate change. Phenotypic traits are the result of interactions between genetic, environmental, and management factors, and dynamic models are designed to generate the interactions producing phenotypic changes over the growing season. Crop phenotype data are becoming increasingly available at various levels of granularity, both spatially (landscape) and temporally (longitudinal, time-series) from proximal and remote sensing technologies. Methods: Here we propose four phenomenological process models of limited complexity based on differential equations for a coarse description of focal crop traits and environmental conditions during the growing season. Each of these models defines interactions between environmental drivers and crop growth (logistic growth, with implicit growth restriction, or explicit restriction by irradiance, temperature, or water availability) as a minimal set of constraints without resorting to strongly mechanistic interpretations of the parameters. Differences between individual genotypes are conceptualized as differences in crop growth parameter values. Results: We demonstrate the utility of such low-complexity models with few parameters by fitting them to longitudinal datasets from the simulation platform APSIM-Wheat involving in silico biomass development of 199 genotypes and data of environmental variables over the course of the growing season at four Australian locations over 31 years. While each of the four models fits well to particular combinations of genotype and trial, none of them provides the best fit across the full set of genotypes by trials because different environmental drivers will limit crop growth in different trials and genotypes in any specific trial will not necessarily experience the same environmental limitation. Discussion: A combination of low-complexity phenomenological models covering a small set of major limiting environmental factors may be a useful forecasting tool for crop growth under genotypic and environmental variation.

Application of one-step method to parameter estimation in ODE models.

In this paper, we study application of Le Cam's one-step method to parameter estimation in ordinary differential equation models. This computationally simple technique can serve as an alternative to numerical evaluation of the popular non-linear least squares estimator, which typically requires the use of a multistep iterative algorithm and repetitive numerical integration of the ordinary differential equation system. The one-step method starts from a preliminary n -consistent estimator of the parameter of interest and next turns it into an asymptotic (as the sample size n→∞) equivalent of the least squares estimator through a numerically straightforward procedure. We demonstrate performance of the one-step estimator via extensive simulations and real data examples. The method enables the researcher to obtain both point and interval estimates. The preliminary n -consistent estimator that we use depends on non-parametric smoothing, and we provide a data-driven methodology for choosing its tuning parameter and support it by theory. An easy implementation scheme of the one-step method for practical use is pointed out.