Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development
Mingdong Zhu,
Meng Zhang,
Kunyong Huang,
Feifei Lu,
Hong Wang,
Shaolu Zhao,
Yinghong Yu,
Shaoqing Tang,
Haining Wu,
Peisong Hu,
Xiangjin Wei
Affiliations
Mingdong Zhu
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China; State Key Laboratory of Hybrid Rice, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan, China
Meng Zhang
Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, Hunan, China
Kunyong Huang
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
Feifei Lu
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
Hong Wang
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
Shaolu Zhao
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
Yinghong Yu
State Key Laboratory of Hybrid Rice, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan, China
Shaoqing Tang
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
Haining Wu
Hubei University, Wuhan 430062, Hubei, China
Peisong Hu
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China; Corresponding authors.
Xiangjin Wei
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China; Corresponding authors.
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.
