Auxin promotes robust founder cell specification during Arabidopsis lateral root initiation

Cell-to-cell variation in gene expression can be highly detrimental and, in some contexts, is actively buffered out; however, in other contexts, it is crucial and actively amplified. For example, variation must be minimized to build organs with consistent size and shape, yet the initiation of organogenesis requires a subset of cells to take on a new fate, a process that often relies on small differences between cells. In plants, much of development is controlled by the hormone auxin, which has been hypothesized to coordinate cell responses by inducing degradation of transcriptional repressors. To quantify the level of variation in lateral root initiation and directly test its connection to auxin signaling, we assessed variation in expression of a lateral root founder cell marker GATA23 when auxin levels or responsiveness was modulated. We found that auxin promoted robustness in lateral root founder cell number in Arabidopsis thaliana, as interfering with auxin signaling resulted in more variable numbers of founder cells and, counterintuitively, an increased average number of founder cells per lateral root. These differences were eliminated when using an integrase recorder of GATA23 expression with an imposed expression threshold instead of a traditional transcriptional reporter. These results led us to posit that auxin acts as both an amplifier and a constrainer of variation during the initiation of a new root. To observe phenotypic effects in a naturally noisier context, we extended this work to analysis of root regeneration, where auxin was also found to affect the robustness of outcomes.