Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions

Abstract

In this study, targeted metabolome analysis was applied to identify the discriminative metabolites between Indonesian shallot landraces, Japanese long-day onion (LDO) varieties, and Japanese short-day onion (SDO) varieties. In total, 172 metabolite signal intensities were subjected to multivariate PLS-DA, VIP, and random forest modeling to gain further insight into genotype-specific metabolites. PLS-DA divides the examined genotypes into three different clusters, implying that shallot landraces exhibited a distinct metabolite profile compared with Japanese LDO and SDO varieties. The PLS-DA, VIP, and random forest results indicated that the shallot and LDO are richer in metabolite constituents in comparison with the SDO. Specifically, amino acids and organosulfur compounds were the key characteristic metabolites in shallot and LDO genotypes. The analysis of S-alk(en)yl-L-cysteine sulfoxide (ACSO) compounds showed higher accumulation in the shallot landraces relative to LDO and SDO varieties, which explains the stronger pungency and odor in shallots. In addition, the LDO showed higher ACSO content compared with the SDO, implying that long-day cultivation might enhance sulfur assimilation in the Japanese onion. The LDO ‘Super Kitamomiji’ and the shallots ‘Probolinggo’ and ‘Thailand’ showed higher ACSO content than other varieties, making it useful for Allium breeding to improve the flavor and stress tolerance of onions.

Antibacterial activity of Shallots (Allium xwakegi Araki.) cultivars in Palu Valley against Salmonella Typhi ATCC 27870 through in vitro and in silico evaluation

“…According to the previous study ( 17 ), the shallot crude extract contains a complex mixture of many plant metabolites, such as alkaloids, glycosides, phenolics, terpenoids, and flavonoids, that can have potential as antibiotics. In line with other research ( 27 , 28 ), these compounds were found in Allium species and were found to have strong antimicrobial properties against bacteria, fungi, and viruses that infect humans. Based on the test results, it can be concluded that phytochemical compounds may have antimicrobial effects.…”

“…The research related to the composition of shallots is still being explored. This is due to differences in varieties, climate, geography, soil fertility, and cultivation practices, which play an important role in the proportion of compounds in shallots ( 28 ).…”

Relevance of genetic and active ingredient content differences in Leonurus japonicus Houtt from different origins

“…PLS-DA, a well-known technique for feature extraction and discriminant analysis in chemometrics, is used to reveal important patterns related to physiological, genetic, and environmental issues. PLS-DA generates visual scatter plots for the qualitative evaluation of variability among multivariate data, and it is now widely used to assess differences among plant species at the metabolome level (Matsuse et al 2022;Zhao et al 2022a). The PLS-DA (R 2 X = 0.9998) was used to analyze the HPLC data.…”