An environmentally responsive dichotomy in cell lineages of the root

Plant development is extremely flexible compared to animals, with growth and architecture being continuously shaped by environmental cues. Roots, for instance, adapt their development to the substrate they are anchored to, water and nutrient availability, and the local biome. This plasticity suggests that, at the cellular level, environmental inputs have a substantial impact on cell function and activity. The root is currently viewed as a collection of distinct cell types, organized in stereotypical layers, each arising from stem cells along a linear differentiation trajectory, much like animal lineages. Cells within each layer are often regarded as mostly homogeneous, with a cell type-specific transcriptional signature that gradually shifts as differentiation progresses. Using single-cell RNA-seq combined with spatial mapping, we deeply explored the trajectories of developing cell type lineages at the tip of Arabidopsis roots. Contrary to the current model of cell identity acquisition in the root, we found that most lineage trajectories exhibit a stereotyped bifid topology, with two developmental paths rather than one. One of these paths is characterized by a strong and specific activation of genes involved in responses to environmental stimuli, including those activating the abscisic acid (ABA) pathway. This state affects only a subset of cells in multiple cell types simultaneously, revealing an additional layer of patterning that is independent of ontogeny. This environmentally responsive transcriptional state is robust, persisting in a mutant with disrupted cell type identities, and consistently present across different Arabidopsis ecotypes, and atlases. Furthermore, we show that its establishment is impaired in ABA-deficient and ABA-insensitive mutants. Finally, we demonstrate that the root can adjust the proportion of cells that acquire this state when grown in a model of drought. The discovery of this alternate fate trajectory, induced by a highly active and environmentally responsive cell state, reveals an additional layer of root cell identity that may underpin the adaptability of roots to challenging environments. Single cell RNA-seq profiling of Arabidopsis thaliana root tips from wild-type accessions, mutants, and different growth conditions: Col-0 full MS (x6), Col-0 half MS (x3), Cvi (x3), Ler (x3), Ws-2 (x3), C24 (x3), aba2-3 (x3), pyl11458 (x3), scr-3 (x3), Col-0 control drought (x2), Col-0 drought 50% water (x2), Col-0 drought 20% water (x2).