Transcriptome revealed the molecular mechanism of Glycyrrhiza inflata root to maintain growth and development, absorb and distribute ions under salt stress

BACKGROUND: Soil salinization extensively hampers the growth, yield, and quality of crops worldwide. The most effective strategies to counter this problem are a) development of crop cultivars with high salt tolerance and b) the plantation of salt-tolerant crops. Glycyrrhiza inflata, a traditional Chinese medicinal and primitive plant with salt tolerance and economic value, is among the most promising crops for improving saline-alkali wasteland. However, the underlying molecular mechanisms for the adaptive response of G. inflata to salinity stress remain largely unknown. RESULT: G. inflata retained a high concentration of Na(+) in roots and maintained the absorption of K(+), Ca(2+), and Mg(2+) under 150 mM NaCl induced salt stress. Transcriptomic analysis of G. inflata roots at different time points of salt stress (0 min, 30 min, and 24 h) was performed, which resulted in 70.77 Gb of clean data. Compared with the control, we detected 2645 and 574 differentially expressed genes (DEGs) at 30 min and 24 h post-salt-stress induction, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that G. inflata response to salt stress post 30 min and 24 h was remarkably distinct. Genes that were differentially expressed at 30 min post-salt stress induction were enriched in signal transduction, secondary metabolite synthesis, and ion transport. However, genes that were differentially expressed at 24 h post-salt-stress induction were enriched in phenylpropane biosynthesis and metabolism, fatty acid metabolism, glycerol metabolism, hormone signal transduction, wax, cutin, and cork biosynthesis. Besides, a total of 334 transcription factors (TFs) were altered in response to 30 min and 24 h of salt stress. Most of these TFs belonged to the MYB, WRKY, AP2-EREBP, C2H2, bHLH, bZIP, and NAC families. CONCLUSION: For the first time, this study elucidated the salt tolerance in G. inflata at the molecular level, including the activation of signaling pathways and genes that regulate the absorption and distribution of ions and root growth in G. inflata under salt stress conditions. These findings enhanced our understanding of the G. inflata salt tolerance and provided a theoretical basis for cultivating salt-tolerant crop varieties. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-03342-6.