Widely Targeted Metabolomics Reveals Metabolic Differences Between Yellow and Brown Flaxseed Cultivars (Linum usitatissimum L.)

Flaxseed (Linum usitatissimum L.) is widely recognized as a functional food due to its rich nutritional composition; however, the metabolic basis underlying seed coat color variation remains unclear. In this study, we performed a broad-targeted metabolomics analysis of six flaxseed varieties (three brown and three yellow) grown at two distinct geographical locations. A total of 1456 metabolites were identified, among which flavonoids and phenolic acids were the most abundant differentially accumulated compounds. Eight metabolites consistently exhibited the largest differences across all comparison groups, and thus warrant further investigation as candidate markers in genetically controlled populations. Correlation analysis further indicated that these metabolites are associated with seed coat pigmentation and other developmental processes. Pathway enrichment revealed that the biosynthesis of caffeic acid derivatives, ferulic acid derivatives, and flavones/flavonols was differentially regulated between yellow and brown seeds. Collectively, our findings provide a comprehensive metabolomic landscape of colored flaxseeds and provide a foundation for future studies aimed at breeding flaxseed varieties with targeted color and nutritional traits.