Metabolome and transcriptome integration provide insights into petal color variation of Chrysanthemum indicum.

Anthocyanins and carotenoids are essential for plant color formation and play significant roles in various physiological processes. This study explores the underlying molecular mechanisms of petal color variation in two Chrysanthemum indicum. Targeted metabolomics quantified 57 carotenoids, revealing higher total carotenoid content in yellow petals than in white petals. The yellow-petaled C. indicum flowers exhibited higher levels of key carotenoids, including lutein dipalmitate, lutein distearate, where total carotenoid accumulation was markedly reduced in white-petaled flowers. In addition, flavonoid profiling identified 544 metabolites, Cyanidin-3-O-(6’’-O-p-Coumaroyl) glucoside was the main color constituent in yellow-petaled C. indicum, while comparative analysis revealed significantly reduced accumulation levels of 10 anthocyanins in the white-petaled C. indicum flowers. Transcriptome analysis revealed that the white-petaled C. indicum flowers is primarily due to the upregulation of carotenoid degradation genes, particularly CiCCD4, which leads to a loss of carotenoids despite active biosynthesis. The yellow petal color is a result of the upregulation of carotenoid biosynthetic genes, such as CiDXS2, and the significant accumulation of specific anthocyanins. Further analysis identified critical structural genes, such as CiDXS and CiPSY, along with transcription factors that likely regulate carotenoid biosynthesis. Furthermore, the structural genes Ci4CL1, Ci3GT, and the transcription factor CiDBB2 may play significant roles in regulating petal color. This study provides a theoretical basis for understanding the phenotypic differences between the petal colors and offers valuable insights into the cultivation and breeding of C. indicum.