Single‐Cell RNA Sequencing Reveals the Developmental Landscape of Wheat Roots

ABSTRACT Allohexaploid wheat ( Triticum aestivum L.) is one of the major crops worldwide, however there is very limited research on the transcriptional programmes of underlying cell type specification. Single‐cell RNA sequencing (scRNA‐seq) was used to unravel the transcriptome heterogeneity of cells and the composition of cell types in broad‐spectrum organisms. Here, we reported the scRNA‐seq transcriptomes of single cells from root tips of the wheat Chinese spring (CS) cultivar, defined cell‐type‐specific marker genes, and identified most of the major cell types. We further profiled the reconstructed developmental trajectories of the stem cell niche (SCN), proximal meristems and meristems, unveiled gene expression signature of water transportation, divulged cell‐type‐specific asymmetric gene transcription in subgenomes and explored the evolutionary conservation and divergence of wheat cultivar (CS) and rice cultivar (Nip and 93‐11, ZH11) cell types through interspecies comparison. Collectively, this work underscored the transcriptional landscape of wheat cultivar (CS) roots and provided a single‐cell perspective for differentiation trajectory application, unbalanced gene expression pattern and characteristics of cell types between two plant species, contributing to a better understanding of wheat cultivar (CS) root development at unprecedented resolution.