Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform

Abstract

Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.

Optimizing photorespiration for improved crop productivity

“…Modelling manipulations to photorespiration also can provide unexpected results, such as how changes in photorespiration could affect nitrogen use, which is integral to the role of photorespiration in maintaining photosynthetic efficiency during NH 3 re‐assimilation. Indeed, large scale computational modelling projects have been created to better design next generation crops (Zhu et al ; Marshall‐Colon et al ; Busch et al ).…”

Predicting metabolism during growth by osmotic cell expansion

“…GrOE-FBA could therefore help complement current kinetic models of guard cells (Hills et al, 2012) with a more holistic modelling approach. Recently, there has been increased interest in combining metabolic models with whole plant developmental models (Marshall-Colon et al, 2017). Growth of sink tissues in the metabolic component of many whole plant models is currently represented solely by the accumulation of biomass components.…”

Simulated Plant Images Improve Maize Leaf Counting Accuracy

“…The first is to improve the accuracy of synthetic plant images. The commercially available procedural model employed here was sufficient for proof of concept, however there is a great deal of scope for further improvements in biological accuracy including the corporation of gene networks and weather models [36], as well as simulating how plants grow and interact with their environments over time [37,38] to produce final adult structures more comparable to those observed in real-world plants. The second is to experiment with a wider range of potential models.…”