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Flavonoids are major bioactive phytochemicals closely associated with plum pigmentation and phytochemical properties; however, the metabolic mechanisms linking flavonoid variation to fruit color divergence remain unclear. Here, unbiased, widely targeted UHPLC MS\/MS metabolomics was employed to comprehensively characterize tissue-specific (peel and flesh) and cultivar-dependent metabolic differences in three plum cultivars with distinct green, yellow, and red peel phenotypes. A total of 981 metabolites were successfully identified. Flavonoid biosynthesis was confirmed as the core pathway regulating tissue- and cultivar-specific metabolic divergence in plums. Reprogrammed flavonoid metabolic flux caused distinct accumulation of characteristic bioactive components, forming two distinct metabolite-based chemotypes: butein-dominant red plums and luteolin 7-glucoside-enriched yellow plums. Spatial metabolite profiling further confirmed the plum peel as the predominant tissue for flavonoid synthesis and accumulation, largely shaping phenotypic color differentiation and phytochemical variation. These findings clarify the intrinsic correlation between flavonoid profiles, visual appearance, and phytochemical characteristics of plum fruit, providing reliable metabolomic evidence for plum germplasm screening, quality evaluation, and resource utilization in the food industry.<\/jats:p>","DOI":"10.3390\/foods15173127","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T09:20:43Z","timestamp":1788427243000},"page":"3127","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Metabolomics Reveals Flavonoid Profiles and Metabolite-Based Chemotypes in Plum (Prunus salicina Lindl.) Fruits with Different Colors"],"prefix":"10.3390","volume":"15","author":[{"given":"Junwei","family":"Liu","sequence":"first","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Jiayi","family":"Li","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Shengcheng","family":"Lin","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Tingting","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Junning","family":"Gong","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Jiaqi","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"}]},{"given":"Aoqi","family":"Xue","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"}]},{"given":"Shishi","family":"Luo","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"}]},{"given":"Yuanyuan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"}]},{"given":"Binqi","family":"Li","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1795-3030","authenticated-orcid":false,"given":"Sheng-Yen","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9655-5868","authenticated-orcid":false,"given":"Faxing","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9036-8006","authenticated-orcid":false,"given":"Honghong","family":"Deng","sequence":"additional","affiliation":[{"name":"College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s00606-007-0539-9","article-title":"Phylogeny and Classification of Rosaceae","volume":"266","author":"Potter","year":"2007","journal-title":"Plant Syst. 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Foods, 12.","DOI":"10.3390\/foods12203801"}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/17\/3127\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T09:51:46Z","timestamp":1788429106000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/17\/3127"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,3]]},"references-count":43,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["foods15173127"],"URL":"https:\/\/doi.org\/10.3390\/foods15173127","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,3]]}}}