Computational Root Biology: Illuminating Patterning and Growth Decisions

Root development arises from the complex interplay between hormonal-genetic control networks, tissue growth and mechanics, with relevant processes ranging from the millisecond to the day and the subcellular to the whole plant scale. Essentially, these processes together enable developmental decision making, for example, whether cells should divide or differentiate, and what cell fate to acquire. Cell-centred computational models have increasingly become a crucial part of root developmental studies. The capacity of models to integrate experimental findings makes them uniquely suited to determine whether thus far deciphered key players are necessary and sufficient to mechanistically explain a phenomenon, to reveal emergent properties and how they come about from constituent parts and to help focus experimental efforts in the direction of missing knowledge. In this chapter, we first provide an overview of the building blocks that make up root tip models, as well as the major variants used for these building blocks with their different drawbacks and advantages. Next, we discuss through a series of example studies how root tip models have contributed to our understanding of root developmental decision-making processes. We end with a series of open questions and suggestions for the type of future modelling studies needed to answer these.