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Salinity stress has become an increasing threat to food security worldwide and elucidation of the mechanism for salinity tolerance is of great significance. Induced mutation, especially spaceflight mutagenesis, is one important method for crop breeding. In this study, we show that a spaceflight-induced wheat mutant, named  salinity tolerance 1  ( st1 ), is a salinity-tolerant line. We report the characteristics of transcriptomic sequence variation induced by spaceflight, and show that mutations in genes associated with sodium ion transport may directly contribute to salinity tolerance in  st1 . Furthermore, GO and KEGG enrichment analysis of differentially expressed genes (DEGs) between salinity-treated  st1  and wild type suggested that the homeostasis of oxidation-reduction process is important for salt tolerance in  st1 . Through KEGG pathway analysis, “Butanoate metabolism” was identified as a new pathway for salinity responses. Additionally, key genes for salinity tolerance, such as genes encoding arginine decarboxylase, polyamine oxidase, hormones-related, were not only salt-induced in  st1  but also showed higher expression in salt-treated  st1  compared with salt-treated WT, indicating that these genes may play important roles in salinity tolerance in  st1 . This study presents valuable genetic resources for studies on transcriptome variation caused by induced mutation and the identification of salt tolerance genes in crops.

RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant