Physiology-Informed Sparse Identification of Dynamic Crop Models

Abstract

Developing resilient crops requires models that accurately capture how plant growth dynamics emerge from the continuous interplay between genetic and environmental factors. While high-throughput phenotyping platforms generate data for dynamic growth models, current modelling approaches show limitations: process-based crop growth models (CGMs) capture environmental dynamics but are difficult to scale across many genotypes because they require calibration of many parameters, while quantitative genetic models allow modelling many genotypes but often summarise time-varying environments using static covariates. To address this gap, we propose a data-driven framework to identify reduced systems of ordinary differential equations (ODEs) describing crop growth dynamics as functions of environmental variables and a controllable number of genotype-specific coefficients (GSCs). Using the Sparse Identification of Nonlinear Dynamics (SINDy) method, we infer model structure directly from data via sparse regression on a physiologically informed library of candidate functions. In this framework, GSCs parameterise cultivar-specific differences in response to environmental conditions. The resulting models are linear in these GSCs, making them compatible with mixed-model and genomic prediction approaches. We evaluate the approach on an in silico dataset generated with WOFOST for five potato cultivars across twelve growing seasons. Our identified ODEs generalise to held-out years and achieve $R^2 > 0.9$ for end-of-season yield prediction across held-out years when compared to full-scale WOFOST simulations. These results provide a proof of concept for SINDy-based identification of parsimonious dynamic crop models from longitudinal crop-growth data.