Multi-omics Analysis of Compositional Differences and Quality Mechanism in Four Color Forms of Gastrodia elata

Gastrodia elata, a valuable Chinese medicinal herb, has multiple color morphs. The quality mechanism of its market-preferred black morph and compositional differences among morphs remain unclear. Thus, this study systematically explored compositional variations among four color morphs black, red, green, yellow of Gastrodia elata f. elata and the high-quality mechanism of black G. elata via nutritional analysis, metabolomics, proteomics, and transcriptomics. Results showed that black G. elata had significantly higher crude protein, soluble protein, and polysaccharide contents than the other three morphs; its crude protein content was 21%, 15%, and 16% higher than that of green, red, and yellow morphs, respectively. Metabolomics identified 1467 metabolites in total, with black G. elata specifically enriched in lipid metabolites such as lysophosphatidylcholines LysoPC. Integrated multi-omics analysis metabolomics, RNA-seq, proteomics indicated that the starch and sucrose metabolism pathway ko00500 differed between black G. elata and other morphs. Moreover, proteomics revealed that high expression of TianMaₜranscript₂3825. p1, which regulates glucosidase activity, may allocate carbon sources to lipid synthesis. Differences in the starch-sucrose pathway endow black G. elata with a unique energy storage process, explaining its rich taste via significant lipid accumulation and linking energy metabolism to G. elata quality. These findings clarify the material basis and molecular mechanism of black G. elata's high quality, providing a scientific basis for germplasm evaluation and new cultivar development of G. elata.