Comprehensive Characterization of Metabolites in Multiplier Onion Bulbs and Identification of Regulatory Genes for Nutritional Improvement

Multiplier onion (<i>Allium cepa</i> var. <i>aggregatum</i>) is an economically important Allium crop that serves dual purposes as both a culinary ingredient and medicinal resource. Despite its widespread utilization, systematic characterization of its nutrient metabolism components remains limited, which has constrained the development of high-value cultivars with optimized nutritional profiles. In this study, we conducted a comprehensive metabolomic profiling of bulbs from five genetically distinct accessions using a widely targeted metabolomic method based on ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The analysis identified 659 metabolites, including lipids, flavonoids, phenolic acids, amino acids, saccharides and alcohols, organic acids, alkaloids, nucleotides and derivatives, vitamins, etc. Notably, the bulbs exhibited a high abundance of flavonoids (e.g., quercetin, kaempferol, naringenin, isorhamnetin) and eight essential amino acids (valine, threonine, leucine, isoleucine, lysine, methionine, histidine, and tryptophan). Comparative analysis revealed that 366 differentially accumulated metabolites were identified among these 5 accessions, many of which were significantly enriched in pathways related to flavonoid biosynthesis, as well as amino acid biosynthesis and metabolism. Transcriptome analysis indicated that differentially expressed genes (DEGs) across the five accessions were significantly enriched flavonoid biosynthesis, and various amino acid biosynthesis and metabolism processes, such as "tyrosine metabolism", "phenylalanine, tyrosine, and tryptophan biosynthesis", "cysteine and methionine metabolism" and "arginine and proline metabolism", being consistent with the substantial variations observed in flavonoids, amino acids, and their derivatives in the metabolome analysis. Correlation and network analysis identified several crucial candidate regulatory genes for the biosynthesis and metabolism of lipids, flavonoids, phenolic acids, and amino acids. These findings provide a comprehensive metabolic atlas of multiplier onion, reveal key genetic regulators of nutritional quality, and establish a scientific foundation for nutraceutical development and cultivar improvement strategies.