Integrated transcriptomics and metabolomics analyses provide insights into cold stress response in wheat

Cold tolerance of crop plants influences survival and productivity under low-temperature conditions. Elucidation of molecular mechanisms underlying low temperature tolerance could be helpful in breeding. In this study, we used integrated transcriptomics and metabolomics analyses to investigate changes in gene/metabolite activity in a winter-hardy wheat cultivar of (cv. Jing 411) when subjected to sold stress. The 223 metabolites mainly enriched during cold acclimation included carbohydrates, flavonoids, and amino acids. Eight common metabolites had altered abundance following freezing treatment; six increased and two decreased. Transcriptome analysis revealed that 29,066 genes were differentially expressed in wheat crowns after cold acclimation compared to the non-acclimated control. Among them, 745 genes were up-regulated following freezing treatment, suggesting substantial change in expression of a large quantity of genes upon cold acclimation and freezing treatment, which impacts on the modified metabolites. Integrated analysis of gene expression and metabolite profiles revealed that the abscisic acid (ABA)/jasmonic acid (JA) phytohormone signaling and proline biosynthesis pathways were significantly modulated under cold acclimation and freezing treatments. Our results indicated that low-temperature stress induced substantial changes in both transcriptomes and metabolomes. Critical pathways associated with ABA/JA signaling and proline biosynthesis played important roles in regulating cold tolerance in wheat.