Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions
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 P...
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| Format: | Article |
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MDPI AG
2022-12-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/12/12/1260 |
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| author | Kanako Matsuse Mostafa Abdelrahman Nur Aeni Ariyanti Fumitada Tsuji Sho Hirata Tetsuya Nakajima Muneo Sato Masami Yokota Hirai Benya Manochai Masayoshi Shigyo |
| author_facet | Kanako Matsuse Mostafa Abdelrahman Nur Aeni Ariyanti Fumitada Tsuji Sho Hirata Tetsuya Nakajima Muneo Sato Masami Yokota Hirai Benya Manochai Masayoshi Shigyo |
| author_sort | Kanako Matsuse |
| collection | DOAJ |
| description | 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 <i>Allium</i> breeding to improve the flavor and stress tolerance of onions. |
| first_indexed | 2024-03-09T16:06:23Z |
| format | Article |
| id | doaj.art-9c2186379f2e4373a382305aa22afbf5 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-09T16:06:23Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-9c2186379f2e4373a382305aa22afbf52023-11-24T16:38:29ZengMDPI AGMetabolites2218-19892022-12-011212126010.3390/metabo12121260Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb OnionsKanako Matsuse0Mostafa Abdelrahman1Nur Aeni Ariyanti2Fumitada Tsuji3Sho Hirata4Tetsuya Nakajima5Muneo Sato6Masami Yokota Hirai7Benya Manochai8Masayoshi Shigyo9Division of Yamaguchi University and Kasetsart University Joint Master’s Degree Program in Agricultural and Life Sciences, Yamaguchi University, Yamaguchi 753-8515, JapanMolecular Biotechnology Program, Faculty of Science, Galala University, Suze 34511, EgyptDepartment of Biology Education, Faculty of Mathematics and Natural Sciences, Universitas Negeri, Yogyakarta 55281, IndonesiaInstitute of Food Sciences and Technologies, Ajinomoto Co., Inc., 1-1 Suzukichō, Kawasaki 210-8681, JapanLaboratory of Agroecology, Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, JapanLaboratory of Vegetable Crop Science, Division of Life Science, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, JapanRIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Yokohama 230-0045, JapanRIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Yokohama 230-0045, JapanDepartment of Horticulture, Faculty of Agriculture, Kasetsart University, Bangkok 10900, ThailandDivision of Yamaguchi University and Kasetsart University Joint Master’s Degree Program in Agricultural and Life Sciences, Yamaguchi University, Yamaguchi 753-8515, JapanIn 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 <i>Allium</i> breeding to improve the flavor and stress tolerance of onions.https://www.mdpi.com/2218-1989/12/12/1260bulb onionsmetabolite profilingshallotssulfur assimilation |
| spellingShingle | Kanako Matsuse Mostafa Abdelrahman Nur Aeni Ariyanti Fumitada Tsuji Sho Hirata Tetsuya Nakajima Muneo Sato Masami Yokota Hirai Benya Manochai Masayoshi Shigyo Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions Metabolites bulb onions metabolite profiling shallots sulfur assimilation |
| title | Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions |
| title_full | Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions |
| title_fullStr | Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions |
| title_full_unstemmed | Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions |
| title_short | Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions |
| title_sort | targeted metabolome profiling of indonesian shallots and japanese long day short day bulb onions |
| topic | bulb onions metabolite profiling shallots sulfur assimilation |
| url | https://www.mdpi.com/2218-1989/12/12/1260 |
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