Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs at this time. Although several studies have reported about organ-specific development and expression induced by light, a systematic analysis of cell-type-specific differentiation and the associated transcriptional regulation is still lacking. Here we obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis thaliana seedlings. Informative cells from shoot and root tissues were grouped into 48 different cell clusters and finely annotated using multiple markers. With the determination of comprehensive developmental trajectories, we demonstrate light modulation of cell fate determination during guard cell specialization and vasculature development. Comparison of expression atlases between wild type and the pifq mutant indicates that phytochrome-interacting factors (PIFs) are involved in distinct developmental processes in endodermal and stomatal lineage cells via controlling cell-type-specific expression of target genes. These results provide information concerning the light signalling networks at the cell-type resolution, improving our understanding of how light regulates plant development at the cell-type and genome-wide levels. The obtained information could serve as a valuable resource for comprehensively investigating the molecular mechanism of cell development and differentiation in response to light.

光是植物的能源，也是植物整个生命周期中生长发育的信号。幼苗去黄化是光调节植物发育过程最引人注目的表现，因为此时植物转录组的大规模重编程发生。尽管有几项研究报道了光诱导的器官特异性发育和表达，但仍然缺乏对细胞类型特异性分化和相关转录调控的系统分析。在这里，我们获得了黄化、去黄化和轻生拟南芥幼苗的单细胞转录图谱。将来自芽和根组织的信息细胞分为 48 个不同的细胞簇，并使用多个标记进行精细注释。通过确定综合发育轨迹，我们证明了保卫细胞特化和脉管系统发育过程中细胞命运决定的光调节。野生型和 pifq 突变体之间的表达图谱比较表明，植物色素相互作用因子 （PIF） 通过控制靶基因的细胞类型特异性表达参与内胚层和气孔谱系细胞的不同发育过程。这些结果提供了有关细胞类型分辨率的光信号网络的信息，提高了我们对光如何在细胞类型和全基因组水平上调节植物发育的理解。所得信息可作为全面研究细胞响应光发育和分化的分子机制的宝贵资源。