Single-nucleus RNA sequencing reveals transcriptional response of wheat roots and leaves to salt stress

Deeper understanding of the mechanism by which wheat responds to salt stress (SS) remains a major challenge due to the scarcity of available single-cell/nucleus transcriptomics resources. Here, in order to uncover the transcriptional patterns during the late stage of SS of different wheat cells, we performed single-nucleus RNA-sequencing (snRNA-seq) on roots and leaves of wheat seedlings under NaCl treatment for 7 d. Integrating snRNA-seq with bulk RNA-seq and physiological and biochemical indices measurement, the single-cell transcriptome atlas of wheat roots and leaves was constructed, and response patterns of cell types to SS were identified based on enrichment of differentially expressed genes for osmotic stress, ion transport, and oxidative stress. Moreover, several cell-type-specific salt-tolerant candidate genes were determined based on pseudotime analysis and functional validation, such as TaWRKY75-A in root hair cells, NICOTIANAMINE SYNTHASE (NAS) genes in root stele I cells, and dehydrin (DHN) genes in leaf fiber cells.