Drought and salinity stress remodel Asian rice (Oryza sativa) leaf development through cell-type specific regulatory programs

The mechanisms through which dividing and differentiating cells perceive, integrate, and respond to stress are not well understood. To explore this knowledge gap, we assessed Asian rice (Oryza sativa) seedling responses to drought and salinity stress by performing single-nucleus transcriptome analyses on developing leaves and by assaying ion distribution using ICP-MS and CoroNa Green staining.

With a dataset of >125,000 high-quality nuclei, we identified transcriptome signatures of developmental trajectories for each of the major tissue systems, from their origin as dividing cells in the shoot apical meristem to mature cells in epidermal, mesophyll, and vascular tissues. We explored the extensive heterogeneity between cell types with respect to their responses to stress by developing an ensemble-based Perturbation Index and a tool for visualizing pseudobulk expression data and characterizing regulatory modules for different stress responses.