Salt stress affects the fruit quality of Lycium ruthenicum Murr.

Halophytic plant Lycium ruthenicum is rich with anthocyanin in fruit, and has thus attracted considerable attention due to its health-promoting effects. However, the effect of salt stress on fruit quality remains unknown. In this study, RNA-seq, LC-MS/MS coupling with TMT labeling, and GC-MS approaches were respectively used to examine the transcriptomic, proteomic, and metabolomic profiles in ripening fruit of 3-year-old trees treated with 0 or 300 mM NaCl, which resulting in 5608 differentially expressed genes (DEGs), 201 differentially expressed proteins (DEPs), and 23 differentially accumulated metabolites (DAMs). KEGG enrichment analysis showed that DEGs related to amino acid metabolism, the TCA cycle, flavonoid biosynthesis, inositol phosphate metabolism, and alpha-linolenic acid metabolism were significantly enriched. DEPs related to protein homeostasis and redox homeostasis were enriched. The contents of anthocyanins, proline, glucose, and glutamine are up-regulated in the salt-treated fruit. Our results indicate that the increased fruit anthocyanin might attribute to the up-regulated MYB component of the MYB-bHLH-WD40 complex and the post-transcriptionally up-regulated proteins encoded by anthocyanin structural genes under salt stress condition. Additionally, weighted gene correlation network analysis (WGCNA) results show that anthocyanin content is highly associated with three modules including multiple transcription factors, genes related to reactive oxygen species homeostasis and phytohormones (abscisic acid and ethylene), and that three FADs genes are involved in the biosynthesis of oleic acid and linoleic acid. Taken together, these findings provide a comprehensive understanding of salt stress-mediated regulation of fruit quality, thereby facilitating the breeding of high anthocyanin cultivars of L. ruthenicum in future.