Integrated Omics Analysis Revealed the Differential Metabolism of Pigments in Three Varieties of Gastrodia elata Bl

<i>Gastrodia elata</i> Blume is a well-known traditional Chinese medicine. The color of flower and flower stalk are important characteristics in the classification of <i>G. elata</i>. However, the mechanisms of pigment formation in different types of <i>G. elata</i> are not yet elucidated. To understand this, targeted metabolomics as well as transcriptomics analyses were carried out in this study. The differential accumulation and the typical components of pigments in different types of <i>G. elata</i> were elucidated. According to our research, the accumulation of carotenoids rather than anthocyanins likely contributes to the pigment content in <i>G. elata</i>. The different accumulations of carotenoids including violaxanthin, lycopene, α-carotene, and α-cryptoxanthin are the main reasons that contribute to the color differences in the flowers and flower stalks of these three <i>G. elata</i> varieties. Integrated multi-omics analysis enriched 50 and 17 differential genes in the flavonoid-anthocyanin and carotenoid biosynthesis pathways, respectively. Among these, <i>PSY</i>, <i>PDS</i>, <i>CCD</i>, <i>UGT</i>, and <i>ANR</i> were identified as critical genes responsible for the differential pigment accumulation in <i>G. elata</i> varieties, while the MYB TFs were tightly associated with main genes expression and content of carotenoids. Overall, this study enhances the current understanding of pigments' metabolites profiles and contributes valuable insights into the molecular mechanisms underlying <i>G. elata</i> carotenoid biosynthesis; these findings also provide valuable guidance for future carotenoid biofortification and molecular breeding in <i>G. elata</i>.