Integrated analysis of transcriptomics and proteomics provides insights into the molecular regulation of cold response in Brassica napus

• Through integrated analysis, the mechanisms of two rapeseed lines with different cold tolerance were explored. • 55 differentially expressed proteins were corresponded to 138 differentially expressed genes. • Photosynthesis, antioxidant enzymes, and energy metabolism are the key responsive pathways under cold stress. • The homologs of selected candidates ( BnCML , BnCAT and BnNIR ) were functionally verified in freezing response. Rapeseed ( Brassica napus L.) is an important edible oil-producing crop worldwide. However, abiotic stresses such as cold in winter can adversely affect plant growth at the seedling stage and subsequently, cause poor seed yield and quality at the mature stage. To understand the underlying molecular mechanisms for cold-stress response in rapeseed, we comprehensively analyzed the profiles of transcripts by using RNA-Seq and proteins by iTRAQ (Isobaric Tag for Relative and Absolute Quantification) in a cold-tolerant (C18) and a cold-sensitive (C6) rapeseed line under cold stress at the four-leaf stage. Based on integrated analysis of transcriptomics and proteomics, 48 differentially expressed genes (DEGs) were found to be corresponded to 17 differentially expressed proteins (DEPs) in C18 during cold stress treatment, whereas 82 DEGs corresponded to 38 DEPs in C6. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that 8 key genes were involved in photosynthesis, followed by 3 in antioxidant enzymes, and 11 in energy metabolism. To verify that these genes function in cold response, Arabidopsis transfer DNA (T-DNA) insertion lines for homologs of the three candidates ( nir , cml , and cat ) were obtained; the three mutant lines differed significantly in levels of freezing response. The integrated analysis here provides insights into molecular mechanisms of the cold response in rapeseed, and valuable information for functional characterization of cold-related genes in rapeseed.