Comparative single-cell RNA-SEQ data analysis under drought stress in rice

Abstract

Drought severity is projected to intensify as global warming raises global surface temperatures. This will impose significant limitations on rice plant growth, development, and productivity, particularly in rain-fed agriculture or in areas where the irrigation system is inadequate. Nevertheless, the tissue-specific mechanisms underlying rice plant responses to water scarcity remain poorly understood. The present study aimed to provide insight into these mechanisms using single-cell RNA sequencing (scRNA-seq) data. The dataset was obtained from the region between the leaf sheath and the stem of 14-day-old rice (Oryza sativa ssp. japonica cv. Kitaake) seedlings grown under normal and drought conditions. For drought treatment, seedlings were first grown under normal conditions for 7 days and then exposed to water-scarcity conditions for an additional 7 days. Based on cell-type-specific gene expression patterns, a minimum of 6 major cell types of rice leaf were annotated. The tissue-specific transcriptional response exhibited that leaf mesophyll cells upregulated genes involved in light responses, carbon fixation, and photorespiration, whereas nucleosome remodeling-related genes were downregulated. In contrast, leaf epidermal cells showed upregulation of genes involved in fatty acid metabolic processes, while genes related to ribosome biogenesis and post-translational modification processes were downregulated. Gene regulatory network inference revealed that the regulon activities of the transcription factors OsERF009, OsERF017, and OsDof21 differed between drought-treated leaf mesophyll and epidermal cells. Specifically, under simulated drought conditions, the regulon activities of OsERF009 and OsERF017 were higher in mesophyll cells; conversely, OsDof21 showed greater activity in epidermal cells. This study demonstrated the key cell-type-specific strategies in rice leaves during the early stages of the response to water deficit, providing new insights into drought-responsive genetic regulation in 14-day-old rice seedlings.