Characterization of cold stress responses in different rapeseed ecotypes based on metabolomics and transcriptomics analysis

Background: Winter oilseed ecotype is more tolerance to low temperature than spring ecotype. Transcriptomes and metabolomes of five spring B. napus ecotype lines and five winter B. napus ecotype lines leaf samples treated at 4℃ and 28℃ were performed.Results: Totally, 25,460 differentially expressed genes (DEGs) in spring oilseed ecotype and 28,512 DEGs in winter oilseed ecotype were identified after cold stress; and there were 41 differentially expressed metabolites (DEM) in spring and 47 in winter oilseed ecotypes. Moreover, more than 46.2% DEGs were common detected in both two ecotypes and the extent of the changes were much more pronounced in winter than in spring ecotypes. While only six DEMs were detected in both spring and winter oilseed ecotypes. Among these 81 DEMs were mainly belong to primary metabolites, including amino acids, organic acids, and sugars. The large number of specific genes and metabolites emphasize the complex regulatory mechanisms involved in cold stress response in oilseed rape. Furthermore, these data suggested the lipid-, ABA-, secondary-metabolism, signal transduction and transcription factors may play the distinct roles between spring and winter ecotypes.Conclusions: Differences in gene expression and metabolite levels after cold stress treatment may have contributed to the cold tolerance of different oilseed ecotypes.