Dynamic transcriptome profiling revealed key genes and pathways associated with cold stress in castor (Ricinus communis L.)

Cold stress causes dwarfism in castor plants and delays development, such that the seeds can not fully mature before the frost occurs. However, little is known about the molecular regulatory mechanisms of cold tolerance in castor. In this study, Illumina RNA-sequencing (RNA-Seq) was used to monitor the dynamic transcriptome changes in the cold-tolerant variety Tongbi 5 when exposed to 4 ℃ for 0, 2, 6, or 8 h. A total of 75, 360, and 711 differentially expressed genes (DEGs) were identified after 2, 6, and 8 h of cold stress, respectively, with the number of upregulated DEGs being much greater than that of downregulated DEGs with the duration of cold treatments. Gene ontology (GO) analysis showed that the nucleus, regulation of transcription, transcription factor activity, DNA binding, metal ion binding, and ubiquitin-protein transferase activity were all enriched. Expression of almost all the transcription factors (TFs) were transcriptionally activated after cold treatment, exhibiting three expression patterns. Moreover, KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that DEGs were significantly involved in Ca2+ signal transduction and mitogen-activated protein kinase (MAPK) cascade pathways, plant circadian rhythm, regulation of autophagy, and plant hormone signal transduction. Combing the identified GO terms, KEGG pathways, and possible DEGs functions, we proposed a “trade-off” model between plant growth and cold tolerance in castor. This study expands our understanding of cold stress responses and provides the excellent gene resources for breeding cold tolerant castor varieties via genetic engineering.