Functional Modeling of Plant Growth Dynamics

Abstract

Recent advances in automated plant phenotyping have enabled the collection time series measurements from the same plants of a wide range of traits over different developmental time scales. The availability of time series phenotypic datasets has increased interest in statistical approaches for comparing patterns of change between different plant genotypes and different treatment conditions. Two widely used methods of modeling growth over time are point-wise analysis of variance (ANOVA) and parametric sigmoidal curve fitting. Point-wise ANOVA yields discontinuous growth curves, which do not reflect the true dynamics of growth patterns in plants. In contrast, fitting a parametric model to a time series of observations does capture the trend of growth, however these models require assumptions regarding the true pattern of plant growth. Depending on the species, treatment regime, and subset of the plant lifecycle sampled this assumptions will not always hold true. Here we introduce a different approach - functional ANOVA - which yields continuous growth curves without requiring assumptions regarding patterns of plant growth. We compare and validate this approach using data from an experiment measuring growth of two maize (Zea mays ssp. mays) genotypes under two water availability treatments over a 21-day period. Functional ANOVA enables a nonparametric estimation of the dynamics of changes in plant traits over time without assumptions regarding curve shape. In addition to estimating smooth curves of trait values over time, functional ANOVA also estimates the the derivatives of these curves - e.g. growth rates - simultaneously. Using two different subsampling strategies, we demonstrate that this functional ANOVA method enables the comparison of growth curves between plants phenotyped on non-overlapping days with little reduction in estimation accuracy. This means functional ANOVA based approaches can allow larger numbers of samples and biological replicates to be scored in a single experiment given fixed amounts of phenotyping infrastructure and personnel.

Plant phenotyping relevance

植物の時系列表現型データから成長曲線と成長率を推定・比較する機能的ANOVAを導入し、実データで検証しているため、表現型解析手法が中心である。

Code and data availability

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