Comparative transcriptome analysis reveals the responses of winter rye to cold stress

Rye is an important economic crop with remarkable resistance to biotic and abiotic stresses and high nutrient utilization. Identification of genes related to cold stress response in winter rye to improve understanding of the molecular mechanism of low temperature response. We performed RNA-seq on winter rye transcriptome under four different cold stress conditions: CK (room temperature), 24 h (4 °C), 48 h (4 °C) and 72 h (4 °C). A total of 128,744 Unigenes were identified, of which 29,874 genes were differentially expressed, including genes related to photosynthesis, plasma membrane stability, glucose and energy metabolism, as well as cold-response transcription factors. GO and KEGG results showed that winter rye protects against low temperature damage by synthesizing extracellular components such as Cutin, suberine and wax. In addition, Oligosaccharides and chitin play a key role in cold resistance of winter rye and MNS1 and MNS3 were the candidate genes. The transcription factors (TFs) results showed that MYB and bHLH families showed a close relationship with cold resistance. In conclusion, the cold tolerance of winter rye is achieved through a variety of biological pathways, including “chitin binding”, “glycolytic process”, and “tricarboxylic acid cycle”. Winter rye can also respond to cold stress by regulating cutin, suberine and wax synthesis. The expression of common cold stress genes such as HSPs, MYBs, bHLHs, NAC, bZIPs, C2H2 and CBF changed after cold stimulation. This study can provide a valuable resource for studies related to cold tolerance, helping to explore genes associated with cold stress and for genetic improvement of crops.