A comprehensive analysis of transcriptomic data for comparison of cold tolerance in two Brassica napus genotypes

Abstract Brassica napus is an important oil crop and cold stress severely limits its productivity. To date, several studies have reported the regulatory genes and pathways involved in cold‐stress responses in B. napus. However, transcriptome‐scale identification of the regulatory genes is still lacking. In this study, we performed comparative transcriptome analysis of cold‐tolerant C18 (CT – C18) and cold‐sensitive C6 (CS – C6) Brassica napus genotypes under cold stress for 7 days, with the primary purpose of identifying cold‐responsive transcription in B. napus. A total of 6061 TFs belonging to 58 families were annotated in the B. napus genome, of which 3870 were expressed under cold stress in both genotypes. Among these, 451 TFs were differentially expressed (DE), with 21 TF genes expressed in both genotypes. Most TF members of the MYB (26), bHLH (23), and NAC (17) families were significantly expressed in the CT – C18 genotype compared with the CS – C6 B. napus genotype. GO classification showed a significant role in transcription regulation, DNA‐binding transcription factor activity, response to chitin, and the ethylene‐activated signaling pathway. KEGG pathway annotation revealed these TFs are involved in regulating more pathways, resulting in more tolerance. In conclusion, the results provide insights into the molecular regulation mechanisms of B. napus in response to freezing treatment, expanding our understanding of the complex molecular mechanisms in plants' response to freezing stress.