An atlas of Brachypodium distachyon lateral root development

The root system of plants is a vital part for successful development and adaptation to different soil types and environments. Besides allowing exploration of the soil for water and nutrients, it also provides anchorage. A major determinant of the shape of a plant root system is the formation of lateral roots, allowing for expansion of the root system. Arabidopsis thaliana, with its simple root anatomy, has been extensively studied to reveal the genetic program underlying root branching. However, to get a more general understanding of lateral root development, comparative studies in species with a more complex root anatomy are required. Brachypodium distachyon is a wild, temperate grass species, that is related to important crops such as wheat. Its roots contain multiple cortex layers and an exodermis that functions as an additional root barrier, besides the endodermis. Here, by combining optimized clearing methods and histology, we describe an atlas of lateral root development in Brachypodium. We show that lateral roots initiate from enlarged phloem pole pericycle cells and that the overlying endodermis reactivates its cell cycle and eventually forms the root cap. In addition, auxin signaling reported by the DR5 reporter was not detected in the phloem pole pericycle cells or young primordia. In contrast, auxin signaling was activated in the overlying cell cortical layers, including the exodermis. Thus, Brachypodium is a valuable model to investigate how signaling pathways and cellular responses have been repurposed to facilitate lateral root organogenesis.