Integrated Metabolomic and Transcriptomic Analyses Reveal Cyanidin as the Key Pigment for Leaf Color Divergence in...

Plants in the Begonia genus are highly valued for their rich leaf color variations, yet the mechanisms underlying leaf color formation in Begonia remain incompletely understood. Two Begonia materials with significantly different leaf colors were selected. The total flavonoid, anthocyanin, and proanthocyanidin contents were measured, and the flavonoid metabolites were analyzed. Meanwhile, RNA-seq technology was employed to compare the transcriptomes of the two materials, and differentially expressed genes (DEGs) related to flavonoid metabolism were identified. There were significant differences in the contents of total flavonoids, anthocyanins, and proanthocyanidins between the two Begonia materials. The accumulation levels of these metabolites were significantly higher in Begonia × hybrida 'Dragon Wing' (Bh, red leaves) than in Begonia longifolia Blume (Bl, green leaves). Color index of red-leaved Begonia was also significantly higher than that of green-leaved Begonia. A total of 185 flavonoid metabolites were identified, with anthocyanin metabolites being significantly accumulated in Begonia × hybrida 'Dragon Wing'. Transcriptome analysis revealed 189 DEGs related to flavonoid metabolism, which were mainly enriched in the pathways of flavonoid biosynthesis and anthocyanin biosynthesis. Further metabolic network analysis indicated that the differential accumulation of cyanidin was the primary cause of leaf color differences between the two Begonia species, and 11 candidate DEGs (including key structural genes DFR and ANS, and putative transcription factors) that may regulate anthocyanin biosynthesis and accumulation were identified. This study provides new insights into the molecular mechanism of leaf color formation and a theoretical basis for breeding Begonia varieties with desirable ornamental color traits.