Integrated transcriptome and metabolome analysis revealed hub genes and metabolites associated with subzero temperature tolerance following cold acclimation in rapeseed (Brassica rapa L.).

Rapeseed naturally endures low temperature in late autumn and early winter to develop cold adaptation, named as cold acclimation (CA). The underlying mechanism by which CA induces plant resistance to subzero temperature tolerance is unclear. This study examined the transcriptome and metabolome of strong (Longyou 7) and weak (Longyou 99) cold-tolerant rapeseed varieties treated with treatments CA and sub-zero temperatures at fourth leaf stage. Cold shock (CS) treatment was developed by incubating seedlings directly at 0, -3, and -7 °C for 4 day at each temperature. For CA, seedlings were acclimatized at 4 °C for one week and then to 0, -3, and -7 °C for four days in each temperature. By transcriptome analysis 5364 and 6534 DEGs were detected in both varieties following CA. Functional enrichment analysis of DEGs showed that carbohydrate metabolism and biosynthesis of secondary metabolic pathways were enriched following CA. A weighted gene co-expression network analysis revealed hub genes AMY2, DREB, MYB, PBL, and GFT1 from three biological modules that can be employed as candidate genes to investigate the network regulation pathway of rapeseed in response to CA treatment. Metabolome profiling revealed phenylalanine, purine, amino sugar and nucleotide sugar, and flavonoid biosynthesis were the most enriched pathways in rapeseed seedlings following CA. Contemporaneous analysis of transcriptomics and metabolomic changes following CA revealed the dynamics of specific gene-metabolite relationships in rapeseed. DEGs and DAMs correlation analysis showed that genes DREB, RAP, TCP2, ZAT12, ASP1, ASP3, ASP4, and the metabolites N-acetyl-D-glucosamine, 2-glycitein, and 3-hydroxybenzyl alcohol glucoside, played an important role in rapeseed following CA. This study's findings elucidate the molecular and regulatory mechanisms enabling rapeseed to withstand subzero temperatures following CA.