Transcriptional Landscape of Arabidopsis Seedling Roots in Response to Simulated Microgravity at Single-Cell Resolution

With the rapid advancement of human space exploration, plants have become indispensable components of space missions, rendering research on microgravity-induced plant responses increasingly pivotal. Eukaryotic multicellular organisms exhibit inherent cellular heterogeneity; therefore, we systematically explored the root responses of Arabidopsis to simulated microgravity via single-cell RNA sequencing (scRNA-seq). We isolated 30,247 high-quality cells from root tips of 10-day-old Arabidopsis seedlings grown under normal conditions or exposed to simulated microgravity and identified 24 distinct cell types via a set of marker genes. Pseudo time trajectory analysis uncovered potential differentiation dynamics within specific cell populations. Notable alterations in cell abundance were observed under simulated microgravity, particularly in lateral root cap (LRC) cells. Enriched in genes associated with stress response, chemical signaling and hormone pathways, LRC cells act as a "microgravity signal sensing and transduction hub," highlighting their core role in environmental stress responses. Simulated microgravity was employed to analyze differentially expressed genes (DEGs) among various cell types, uncovering significant DEGs in specific cell types. Furthermore, a multitude of candidate DEGs associated with transcription factors or plant hormones were identified. Under simulated microgravity, the auxin levels in Arabidopsis root LRC and QC cells were enhanced, with upregulation of YUC3 and other genes. Collectively, we constructed a single-cell transcriptional atlas of Arabidopsis roots under simulated microgravity, providing a valuable resource for investigating cellular heterogeneity and differentiation dynamics in plant responses to microgravity.