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

Kanako Matsuse, Mostafa Abdelrahman, Nur Aeni Ariyanti, Fumitada Tsuji, Sho Hirata, Tetsuya Nakajima, Muneo Sato, Masami Yokota Hirai, Benya Manochai, Masayoshi Shigyo

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


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.

Original languageEnglish
Article number1260
Issue number12
Publication statusPublished - Dec 2022

All Science Journal Classification (ASJC) codes

  • Endocrinology, Diabetes and Metabolism
  • Biochemistry
  • Molecular Biology


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