There are two main types of root systems in flowering plants, namely taproot systems of dicots and fibrous root systems found in monocots. Despite this fundamental split, our current knowledge of cellular and molecular mechanism driving root development is mainly based on studies of the dicot model Arabidopsis. However, the world major crops are monocots and little is known about the transcriptional programs underlying cell-type specification in this clade. Here, we report the transcriptomes of more than 20 000 single cells derived from root tips of two agronomically important rice cultivars. Using combined computational and experimental analyses we were able to robustly identify most of the major cell types and define novel cell-type-specific marker genes for both cultivars. Importantly, we found divergent cell types associated with specific regulatory programs, including phytohormone biosynthesis, signaling, and response, which were well conserved between the two rice cultivars. In addition, we detected substantial differences between the cell-type transcript profiles of Arabidopsis and rice. These species-specific features emphasize the importance of analyzing tissues across diverse model species, including rice. Taken together, our study provides insight into the transcriptomic landscape of major cell types of rice root tip at single-cell resolution and opens new avenues to study cell-type specification, function, and evolution in plants.

开花植物中有两种主要类型的根系，即双子叶植物的主根系统和单子叶植物中的纤维根系统。尽管有这种根本性的分裂，我们目前对驱动根发育的细胞和分子机制的了解主要基于对双子叶植物模型拟南芥的研究. 然而，世界上的主要作物是单子叶植物，并且对该进化枝中细胞类型特化的转录程序知之甚少。在这里，我们报告了来自两个重要农艺栽培品种根尖的 20 000 多个单细胞的转录组。使用联合计算和实验分析，我们能够有力地识别大多数主要细胞类型，并为两种栽培品种定义新的细胞类型特异性标记基因。重要的是，我们发现了与特定调控程序相关的不同细胞类型，包括植物激素生物合成、信号传导和响应，这在两个水稻品种之间得到了很好的保守。此外，我们检测到拟南芥的细胞类型转录谱之间存在显着差异和米饭。这些物种特异性特征强调了分析不同模型物种（包括水稻）组织的重要性。总之，我们的研究以单细胞分辨率深入了解了水稻根尖主要细胞类型的转录组学景观，并开辟了研究植物细胞类型规范、功能和进化的新途径。