Transcriptome changes triggered by a short-term low temperature stress in winter wheat

Abiotic stresses alter the expression of multiple genes in plants allowing them to accommodate to hostile environmental conditions. Exposure to low temperatures in the autumn prior to winter is a crucial environmental factor determining an increase in freezing tolerance and winter hardiness in temperate plants. The objective of this study was to evaluate transcriptome changes under a short-term low temperature stress using an RNA-Seq approach in winter wheat (Triticum aestivum L.). Significant alterations were observed for nuclear transcriptome of winter wheat, whereas the expression profiles of organellar genes were much less responsive to low temperature stress. In total, there were 15,042 nuclear genes with significantly (FDR < 0.05) altered expression profiles caused by exposure to low temperature. From this number, a total of 2,466 genes had a substantially (log 2 FC > 2 or log 2 FC < -2) affected expression profile. The highest number of upregulated genes was observed from chromosomes in homoeologous group 5, followed by group 2. Differentially expressed genes (DEGs) with the most extreme upregulation encompassed CBFIIId-12.1, WRKY transcription factor 55-like, and a group of genes related to jasmonate signalling pathway.