Integrative Analysis of Transcriptome and Metabolome Provides Insights into the Saline-Alkali Stress in Alfalfa

Medicago sativa L. is a widely planted leguminous forage crop with rich nutritional value and is known as the “king of forage”. However, during the growth process of alfalfa, it often suffers from salt stress from the soil, resulting in a serious decline in yield and quality. At present, significant progress has been made in understanding the regulatory mechanism of alfalfa response to neutral salts (NaCl). The salt in the soil contains not only neutral salts but also alkaline salts, and there is still limited understanding of how alfalfa responds to saline-alkali stress. Here, transcriptome and metabolome analysis were performed to reveal the mechanisms related to saline-alkali stress in alfalfa. A total of 19 121 differentially expressed genes (DEGs) were found at 12 h of saline-alkali stress, and 16 515 DEGs were found at 24 h of saline-alkali stress. Moreover, five common biological pathways, namely, “metabolic pathways”, “biosynthesis of secondary metabolites”, “biosynthesis of variable plant secondary metabolites”, “nitrogen metabolism”, and “cysteine and methionine metabolism”, were significantly enriched at different time points, indicating that these five pathways play important roles in the response of alfalfa to saline-alkali stress. Moreover, 133 differential metabolites (DAMs) were identified at 12 h of treatment, and 173 DAMs were identified at 24 h of treatment. Glyoxylate and Dicarboxylate metabolism pathway were significant enriched by integrated analysis of the two different omics. And, 97 DEGs and 6 DAMs were found in this pathway. In addition, RT-PCR was used to further validate the randomly selected DEGs, demonstrating the accuracy of the RNA-seq results. In summary, this study provides valuable information for exploring the response of alfalfa to saline-alkali stress in the future.