Metabolome and transcriptome analysis reveals molecular mechanisms of watermelon under salt stress

Salinity seriously limits crop production worldwide, affecting the growth and development of watermelon. This study explored the regulatory mechanism of watermelon seedlings in response to salt stress through the combined analysis of metabolomics and transcriptomics. Many differentially accumulated metabolites (DAMs) and differently expressed genes (DEGs) were affected by salt stress and observed significant changes. The combined analysis of DAMs and DEGs showed that watermelon seedlings mainly responded to salt stress by regulating amino acid and carbohydrate metabolism pathways. Amino acid metabolites such as L-Glutamate, 4-Aminobutanoate (GABA), and Proline were up-accumulated under salt stress. Carbohydrate metabolites such as Sucrose, D-Glucose, D-Fructose, etc., regulated by genes such as SUS, α-GAL, PFK, PFP, etc., were down-regulated in the early stage (12 h) of salt stress, but were up-accumulated in the later stage (96 h) of salt stress, showed different responses in the early and late stages of salt stress. Salt stress significantly reduced the expression of DEGs in photosynthesis-related pathways. Transcription factors such as AP2/ERF-ERF, MYB, bHLH, NAC, bZIP, also changed significantly in response to salt stress. We identified 7 key DAMs and 21 DEGs and 6 key DAMs and 67 DEGs in amino acid and carbohydrate metabolic pathways, respectively. These findings further explained the mechanism of salt stress in watermelons and aided in breeding salt-resilient watermelon cultivars.