Integrative analysis of transcriptome and metabolome provides insights into the underlying mechanism of cold stress response and recovery in two tobacco cultivars

Low temperature is one of major environmental factors limiting the growth, quality and yield of tobacco. However, the molecular mechanism of tobacco cold response remains largely unknown. Here, integrated biochemical, transcriptomic and metabolomic analyses were carried out on tobacco leaves of cold-tolerant cultivar Xiangyan7 and cold-sensitive cultivar Taiyan8 under short- /long-term cold stress and recovery. Physiological and biochemical results showed that Taiyan8 was sensitive while Xiangyan7 was insensitive to cold stress. Integrated transcriptomics and metabolomics analysis revealed several key pathways in tobacco response to cold, including flavonoid biosynthesis, glutathione metabolism, zeatin biosynthesis, phenylpropanoid biosynthesis, starch and sucrose metabolism; two important pathways in the recovery, namely glyoxylate and dicarboxylate metabolism, flavonoid biosynthesis. The two cultivars had similar mechanisms in response to long-term cold stress. Whereas, more enriched pathways were identified in Taiyan8 under short-term stress, and the specifically enriched pathways were mainly involved in amino acid metabolism. By analyzing the metabolites involved in these pathways, a total of 26 key metabolites were screened out. These metabolites contents and biochemical indicator values were used as trait data for correlation analysis with gene expression modules, and 5 highly correlated modules were found. Within these modules, we identified 12 key candidate genes weighted as module hub genes, which involved ATPases, chlorophyll A-B binding protein, S-adenosine methionine decarboxylase, chalcone and stilbene synthases, UDP-glucosyltransferases, alcohol dehydrogenase, abhydrolase, proteins with ankyrin-repeat domains. The expression profiles of these genes further verified their involvement in tobacco cold response and recovery. These findings provide new insights into the regulatory networks of tobacco response to cold stress.