Transcript and hormone analyses reveal the involvement of ABA-signalling, hormone crosstalk and genotype-specific biological processes in cold‐shock response in wheat

•636 cold‐shock responsive genes were identified in three wheat genotypes.•More up‐ than down‐regulated genes were identified in both freezing‐sensitive and freezing‐tolerant genotypes.•ABA and its metabolites responded oppositely to cold‐shock in all lines.•ABA‐signalling might have a role in cold‐shock response of the examined genotypes.•Genotypes had differences in signal information‐flow and stress‐responsive biological processes.

The effect of one-day cold-shock on the transcriptome and phytohormones (auxin, cytokinins, abscisic, jasmonic and salicylic acids) was characterised in freezing-sensitive (Chinese Spring), highly freezing-tolerant (Cheyenne) and moderately freezing-tolerant (Chinese Spring substituted with Cheyenne's 5A chromosome) wheat genotypes. Altogether, 636 differentially expressed genes responding to cold‐shock were identified. Defence genes encoding LEA proteins, dehydrins, chaperons and other temperature-stress responsive proteins were up‐regulated in a genotype‐independent manner. Abscisic acid was up-regulated by cold accompanied by adherent expression of its metabolic genes. Data revealed the involvement of particular routes within ABA-dependent signalling in response to cold‐shock in the examined genotypes. Cold‐shock affected gene expression along carbohydrate metabolic pathways. In photosynthesis, cold‐shock changed the expression of a number of genes in the same way as it was previously reported for ABA. Overrepresentation analysis of the differentially expressed genes supported the ABA‐signalling and carbohydrate metabolism results, and revealed some pronounced biological process GO categories associated with the cold‐shock response of the genotypes. Protein network analysis indicated differences between the genotypes in the information flow along their signal perception and transduction, suggesting different biochemical and cellular strategies in their reaction to cold‐shock.