Two distinct oscillatory auxin signals define the plasticity of lateral rooting in Arabidopsis thaliana

The so-called root clock defines lateral root pre-branch sites (PBS) but how these sites contribute to the root system architecture remains incompletely understood ^1,2,3,4 . Here we reveal in the model plant Arabidopsis thaliana that two distinct oscillatory systems for the phytohormone auxin coordinate the spatial and temporal identity of PBS, jointly defining the lateral root density. We followed auxin signalling dynamics for days and thereby detected a systemic auxin signal oscillating in the mature primary root, which is distinct from the previously described root clock at the root tip. While the root clock spatially primes the PBS in the growing root tip, the systemic oscillatory auxin signal temporally controls the auxin-dependent identity of these PBS. Light perception in the shoot defines the strength of the systemic auxin signal and thereby controls the auxin-reliant ability of PBS to develop into lateral roots. Moreover, PHYB and CRY1 mediate the light-dependent integration of other environmental signals, such as ambient temperature, into the control systemic auxin signalling and lateral root density. Our work reveals how two spatially distinct oscillatory auxin signals define the plasticity of plant root development in response to fluctuating conditions.