Combining metabolomics and transcriptomics to study selenium response mechanisms in germinating watermelon seeds

Watermelon seeds are readily accepted even after selenium enrichment, thereby potentially helping meet daily selenium requirements of adults. However, no existing studies have elucidated the molecular-level metabolic changes in watermelon seeds induced by selenium enrichment. In this study, UPLC-MS/MS was employed to identify and quantify metabolite alterations in watermelon seeds. A total of 1036 metabolites were identified, and 81 differentially expressed metabolites (DEMs) being screened out. Gene identification and expression analysis were conducted using the Illumina NovaSeq 6000 platform. A total of 18,686 genes were identified, and 999 differentially expressed genes (DEGs) were screened out. Joint omics analysis revealed that DEMs and DEGs were enriched in 25 pathways, primarily involving flavonoid biosynthesis and amino acid metabolism. Genes like PAL, 4CL, CYP73A, and CHS were the key genes for the biosynthesis of flavonoids under selenium treatment, resulting in a significant decrease in the expression level of chlorogenic acid in the pathway. In the amino acid metabolism pathway, genes such as AGXT2, glnA, speE, and thrC played crucial roles, causing significant alterations in the expression levels of metabolites such as L-Alanine, Threonine, and Tryptophan in the pathway. This study provides a theoretical basis for developing watermelon seeds with both selenium-enrichment function and balanced nutrition. The selenium enrichment process can be improved by regulating the expression levels of key genes such as PAL and AGXT2, and the amino acid composition can also be regulated.