The root system is a major determinant of a plant’s access to water and nutrients.The architecture of the root system to a large extent depends on the repeated formation of new lateral roots.In this review,we discuss lateral root development from a systems biology perspective.We focus on studies combining experiments with computational modeling that have advanced our understanding of how the auxin-centered regulatory modules involved in different stages of lateral root development exert their specific functions.Moreover,we discuss how these regulatory networks may enable robust transitions from one developmental stage to the next,a subject that thus far has received limited attention.In addition,we analyze how environmental factors impinge on these modules,and the different manners in which these environmental signals are being integrated to enable coordinated developmental decision making.Finally,we provide some suggestions for extending current models of lateral root development to incorporate multiple processes and stages.Only through more comprehensive models we can fully elucidate the cooperative effects of multiple processes on later root formation,and how one stage drives the transition to the next.