Conjoint transcriptome and metabolome analysis of the response mechanism of flax root to salt stress

In this study, a co-expression analysis of differentially expressed genes and differentially accumulated metabolites in the roots of salt-tolerant (R40) and salt-sensitive flax germplasm (R24) under NaCl stress was conducted through conjoint analysis of the broad-target metabolome and transcriptome. This could help to understand the coordinated variations in the metabolome and key genes, to elucidate the metabolic process and the associated changes in flax under salt stress, and ultimately to identify the important flax genes that might regulate the metabolic pathways related to salt resistance. Here, we identified 741 metabolites with significant differences, including 409 downregulated and 332 upregulated metabolites. We also identified 30 233 differentially expression genes including 15 827 upregulated genes and 14 406 downregulated genes, of which 13 015 transcription factors were annotated. Almost all of the top ten metabolites were enriched with the corresponding functional transcription factors. For example, corresponding transcription factors are involved in flavonoid and flavonol biosynthesis, phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, anthocyanin biosynthesis, flavonoid biosynthesis, and other pathways. The important genes of flax roots regulating salt resistance metabolism under salt stress are mainly involved in regulating sugar metabolism, thus effectively reducing the damage caused by saline-alkali stress by enhancing the osmotic pressure of cells. In the present study, eight candidate genes were significantly correlated with five metabolites, and each metabolite was associated with one or more genes. In addition, the GH3 gene found in the tryptophan-auxin pathway is a typical gene correlated with the primary reaction of auxin and plays important roles in stress resistance and defense responses.