Identification of rare cell types in the single-cell transcriptome of rice - a case study of stomata

In order to preliminarily explore the regulatory mechanism of development and movement of grass stomata, in this study, on the basis of the primary clustering, we successfully obtained independent and stable clusters of guard cells and subsidiary cells from single-cell transcriptome data in rice leaves by sub-clustering analysis of all the obtained epidermal cells when the resolution value of sub-clustering was set at 2.6, combined with more marker genes. They consist of 12 guard cells and 17 subsidiary cells, respectively. GO enrichment analysis revealed the biological processes of late stomatal development such as "microtubule-based movement", “signal transduction” and "response to stimulus". Gene regulatory network analysis revealed genes such as OsDOF11, OsMAPK2, OsNAC75, OsABCG4, OsERF52 and OsSWEET2b and their potential interaction networks. The results of this study provide a methodological reference for the identification of rare cell types in plants, and also provides new marker genes for the study of stomatal cells in other grasses. At the same time, the analysis of the genes that may play important roles in the regulatory networks is of great significance for the analysis of the molecular basis of stomatal development and the cultivation of rice breeding with excellent resistance traits.