Transcriptomic and metabolomic analyses of the response of sainfoin (Onobrychis viciifolia) seedings to low-temperature stress

Sainfoin ( Onobrychis viciifolia ) is a valuable native legume forage in northwest China and is commonly used as fodder for livestock. However, low temperatures (LW) not only affect the yield and quality of sainfoin but also its geographical distribution. The leaves of the cold-tolerant new line of P4 and the cold-sensitive material of 13709 were collected after low temperature (4℃) treatment to evaluate their molecular regulatory mechanisms during low temperature via integrative analyses of their transcriptomes and metabolomes. A comprehensive analysis was conducted, including the detection of 6619 metabolites and annotation of 6939 genes using UPLC-MS/MS analysis and the IIIumina HisSeq system. The metabolomics analysis revealed 26 common differentially accumulated metabolites (DAMs) in the cold-tolerant and cold-sensitive sainfoin at different comparisons, these metabolites are mainly divided into lipids and lipid-like molecules, and phenylpropanoids and polyketides. Transcriptome analysis identified 1045, 1412, 5010, and 3119 differentially expressed genes (DEGs) in different comparisons at the same time points. By integrating the transcriptomic and metabolomic datasets, it was observed that several DAMs were closely associated with DEGs. Functional enrichment analysis of DAMs and associated DEGs highlighted their involvement in anthocyanin biosynthesis and amino acid metabolism. Six candidate genes from the above pathways were selected for controlling the adaptation to LW stress. These findings provide valuable insights into the metabolic regulation of sainfoin under LW stress and offer guidance for improving its cold resistance and selecting cold-tolerant varieties.