| Summary: | Utilizing salt-tolerant plants is a cost-effective strategy for agricultural production on salinized land. However, little is known about the mechanism of dandelion (<i>Taraxacum mongolicum</i> Hand.-Mazz.) in response to saline stress and caffeic acid biosynthesis. We investigated the morphological and physiological variations of two dandelions, namely, “BINPU2” (dandelion A) and “TANGHAI” (dandelion B) under gradient NaCl concentrations (0, 0.3%, 0.5%, 0.7%, and 0.9%), and analyzed potential mechanisms through a comparison analysis of transcriptomes in the two dandelions. Dandelion A had a high leaf weight; high ρ-coumaric acid, caffeic acid, ferulic acid, and caffeoyl shikimic acid contents; and high activities of POD and Pro. The maximum content of four kinds of phenolic acids mostly occurred in the 0.7% NaCl treatment. In this saline treatment, 2468 and 3238 differentially expressed genes (DEGs) in dandelion A and B were found, of which 1456 and 1369 DEGs in the two dandelions, respectively, showed up-regulation, indicating that more up-regulated DEGs in dandelion A may cause its high salt tolerance. Further, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that dandelion salt response and caffeic acid metabolism were mainly enriched in the phenylpropanoid biosynthesis pathway (ko00940) and response to ethylene (GO: 0009723). The caffeic acid biosynthesis pathway was reconstructed based on DEGs which were annotated to <i>PAL</i>, <i>C4H</i>, <i>4CL</i>, <i>HCT</i>, <i>C3′H</i>, and <i>CSE</i>. Most of these genes showed a down-regulated mode, except for parts of DEGs of <i>4CL</i> (TbA05G077650 and TbA07G073600), <i>HCT</i> (TbA03G009110, TbA03G009080, and novel.16880), and <i>COMT</i> (novel.13839). In addition, more up-regulated transcription factors (TFs) of ethylene TFs in dandelion A were found, but the TFs of <i>ERF104</i>, <i>CEJ1</i>, and <i>ERF3</i> in the two dandelions under saline stress showed an opposite expression pattern. These up-regulated genes could enhance dandelion salt tolerance, and down-regulated DEGs in the caffeic acid biosynthesis pathway, especially <i>CSE</i> (TbA08G014310) and <i>COMT</i> (TbA04G07330), could be important candidate genes in the synthesis of caffeic acid under saline stress. The above findings revealed the potential mechanisms of salt response and caffeic acid metabolism in dandelion under saline stress, and provide references for salt-tolerant plant breeding and cultivation on saline–alkali land in the future.
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