Thursday, 11 July 2019

ARTICLE: Getting to the root of the problem

Model selection and parameter estimation for root architecture models using likelihood-free inference
Clare Ziegler, Rosemary J. Dyson, Iain G. Johnston
J Roy Soc Interface (online, doi.org/10.1098/rsif.2019.0293 , 2019)

Roots bridge plants and soil, making vital contributions to crops, the environment, and fundamental biology. Because of this importance, understanding how roots grow under different conditions is a key scientific target. Experimental approaches to study roots can be challenging: being underground, it’s hard to observe root systems without perturbing them. Computer models can help here: we can simulate root growth and the “architecture” of root systems under lots of different conditions, without having to dig up and destroy real plants.


 
Observing roots growing underground is hard, but not impossible: here's a shot from our "minirhizotron" experiments using underground cameras to watch roots grow in an experimental woodland facility (see article here, and 3D version here!)

As computers have become more powerful, more and more sophisticated models for root growth and architecture have emerged. These simulation approaches typically take as input a set of parameters, and produce as output a model root system. These parameters are numbers describing, for example, the rates of root elongation, distances between lateral root branches, and so on – there may be dozens, or hundreds, of parameters in a sophisticated root model.

The output of a model depends strongly on these parameter values. So how can we choose the “right” ones? We may know some from experiments – for example, the widths of roots can be readily measured. But others may be less easy to observe. It is quite common to make educated guesses at these parameters, and see if the resulting root system “looks right”. This approach has a few issues – it can be subjective, and doesn’t give us information on how flexible our guesses are. For example, is a growth rate of 0.1cm per day just as likely as 0.5cm per day, or 0.02cm per day? And how can we tell if one version of a model does “better” than another, and is more supported by real observations?

In a new paper here in Journal of the Royal Society Interface, we propose a platform to provide answers to these questions, using so-called “approximate Bayesian computation” or ABC. This is a way of learning which parameter values and models are most compatible with observed data, by running many simulations with many different choices, and comparing the output of each choice to our observations using specific criteria. This replaces the subjective “looks right” and explores a wide set of parameterisations, allowing us to learn what ranges of values are most likely given our data. We can also use ABC to compare different mechanisms for root growth, finding which is most supported by observation. This helps us gain scientific insight and ensures that the outputs of our models can be more reliably intepreted.


Overview of our approach. Using ABC allows us to identify governing parameters and mechanisms for root growth that are most supported by real observations.

We tested our ABC approach with synthetic observations from models of thale cress and narrowleaf lupin, confirming that we can recover the parameter values we put in. We then used real thale cress plants (wild and mutant) to show that our platform distinguishes genetically different plants and identifies most-likely parameters and model structures for real root growth. We used the platform to select models for growth and branching, showing how it can be used to compare existing models from the literature. We hope that this approach can be used to further help improve the interpretability and rigour of plant modelling and simulation! Iain and Clare

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