Wide-ranging varieties and/or strains of bulb onions (Allium cepa Common onion group) and shallots (A. cepa Aggregatum group) were utilized to understand the variation in chemical compounds responsible for their taste. The bulb samples of 10 F1 commercial onion varieties (seven short-day and three long-day varieties) from Japan and 12 shallot landraces from abroad (Vietnam: three landraces; Indonesia: nine landraces) were collected as plant materials once a year in 2014 and 2015. The contents of S-alk(en)yl-L-cysteine sulfoxides, total flavonoids, and soluble sugars—including fructose, glucose, sucrose, and fructans—were determined to find differences between bulb onions and shallots, as well as to detect variations among varieties and/or landraces. While a principal component analysis (PCA) based on the results from both 2014 and 2015 could clearly discriminate shallots from bulb onions from a phytochemical perspective, bulb onions mainly had higher monosaccharides than shallots. By contrast, shallots produced more disaccharides than bulb onions. In most cases, regression analyses using the numerical data of the chemical compounds found in bulb onions and shallots suggested year-year correlations between 2014 and 2015. The flavonoid and PeCSO (S-(1-propenyl)-L-cysteine sulfoxide: isoalliin) contents in shallots were higher than those detected in bulb onions, which indicated the stronger pungent and bitter taste could be attributable to excess amounts of these compounds in this tropical plant.
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