Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress

Cold stress greatly affects plant growth and crop yield. To identify novel genes and possible mechanisms involved in chilling tolerance responses in rice seedlings, RNA sequencing (RNA-seq) technology was used for genome-wide gene expression profiling analysis to compare three cold-tolerant genotypes and one cold-sensitive genotype under both normal temperature and cold stress treatments. The results showed that in response to cold, a total of 2242 common regulated differentially expressed genes (DEGs) were detected during cold stress in all of the genotypes, and a total of 318 DEGs were detected as common DEGs related to cold tolerance in the three cold-tolerant genotypes. Gene ontology (GO) enrichment analyses were performed for these DEGs. By combining protein function clustering analysis and significantly enriched GO terms analysis, we suggest that calcium signal transduction may play a dominating role in the cold stress response of rice. Further, we suggest that RNA helicases may be directly involved in temperature sensing in rice under cold stress, and that compensation of ATPase activity, alteration of epigenetic processes, and further reduction of functional photosynthesis proteins may serve as mechanisms for cold tolerance regulation in the cold-tolerant rice genotypes. These results expand our understanding of the complex mechanisms involved in chilling tolerance in rice, and provide a foundation for future studies on chilling tolerance in rice and other cereal crops.