The pigmentation of various components leads to different colors of roses. However, the intricate molecular machinery and metabolic pathways underlying rose pigmentation remain largely unexplored. In this study, we determined that pink and black-red petals contain abundant anthocyanins, reaching concentrations of 800 μg/g and 1400 μg/g, respectively, significantly surpassing those in white and yellow petals. We identified 22 key anthocyanin components, predominantly cyanidin, pelargonidin, delphinidin, peonidin, and petunidin, which were preferentially enriched in pink and black-red petals. Additionally, we confirmed the presence of five carotenoid species—lutein, zeaxanthin, ζ-carotene, α-carotene, and β-carotene—with zeaxanthin and carotenoids notably accumulating in yellow petals at significantly higher levels compared with other colors. Furthermore, RNA-seq and qRT-PCR analyses revealed the association between pigment accumulation and the expression patterns of genes involved in anthocyanin and carotenoid biosynthesis pathways. Through promoter core element prediction and transcriptional metabolic co-expression analyses, we found that the MYB transcription factor likely positively modulates the expressions of key biosynthetic genes such as CHS, F3′H, and DFR, while the NAC transcription factor enhances the transcriptional activities of PSY, ZISO, and LYCB. Overall, this study explores the components of flower color, unravels the synthesis of anthocyanins and carotenoids, identifies regulatory factors, and highlights the prospects of rose breeding.

Chongqing Old Rose is an ancient edible rose variety native to Chongqing, China, but is under-reported. Further evidence is required to fully establish its potential benefits. The complete metabolic profiles were examined for comparative analysis between the Old Rose and three rose cultivars. The results showed that the pathways of flavonoid biosynthesis, monoterpenoid biosynthesis, and phenylalanine metabolism were significantly enriched in Old Rose. The predominant anthocyanins in Old Rose were cyanidin and peonidin, which may contribute to flower coloration and indicate the antioxidant potential of this plant. Additionally, this plant was rich in aromatic compounds and terpenoids such as 2-phenylethanol, linalool, geraniol, and caryophyllene α-oxide, indicating that it has a natural basis for extracting essential oil. Moreover, the presence of some active phytoconstituents, such as phenols, steroids, and alkaloids, also suggests its potential for edible and medicinal applications besides flavonoids and terpenoids.

Rosa species hold considerable economic and medicinal importance, used in traditional medicine, essential oils, and landscaping. However, the mechanisms of floral scent formation in roses are not well understood, hindering genetic improvement. To bridge this gap, we conducted a combined transcriptome and metabolome analysis, identifying nine key fragrance compounds. Using Weighted Gene Co-expression Network Analysis (WGCNA), we linked 574 genes to these compounds. From these, we identified candidate genes through differential expression, functional annotations, and protein-protein interaction (PPI) networks. We predicted candidate genes, NUDIX1, NUDIX2, GERD, AFS1, AFS2, CYP82G1, HMG1, NCED2, CCD7, PSY, ICMEL2, MAD1, and MAD2 that might terpenoid-related genes, as well as potential benzenoid/phenylpropanoid-related candidate genes, DET2, DET3, ICS2, PAL1, UGT74B1, MYB330, GST, CAD1, HST, PCBER1, LAC15, CSE, PER25, PER47, PER63, FBA, LNK2, PRE1, and PRE6. Additionally, three function-unknown genes, LOC112167529, LOC112174760, and LOC112183447, were predicted as candidate genes potentially involved in the formation of floral scent.