Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ morphogenesis. Here, the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17, a popular Chinese indica rice cultivar. Of 15 cell clusters, 13 were assigned to cell types using marker genes and cluster-specific genes. Marker genes of multiple cell types were expressed in several clusters, suggesting a complex developmental system. Some genes for signaling by phytohormones such as abscisic acid were highly expressed in specific clusters. Various cis-elements in the promoters of genes specifically expressed in cell clusters were calculated, and some key hormone-related motifs were frequent in certain clusters. Spatial expression patterns of genes involved in rapid seed germination, seedling growth, and development were identified. These findings enhanced our understanding of cellular diversity and specialization within plumules of rice, a monocotyledonous model crop.