Comparative transcriptome analyses reveal genes related to pigmentation in the petals of a flower color variation cultivar of Rhododendron obtusum

Abstract Rhododendron is an important woody ornamental plant and breeding varieties with different colors is vital research goal. In this study, a flower color variation cultivar ‘Yanzhi Mi’ (pink petals) and the wild-type (WT) cultivar ‘Dayuanyangjin’ (white petals with pink stripes) were used as research objects, the pigment and transcriptome of their petals during different flower development (stage S1, S2, S3, S4 and S5) were analyzed and compared. The results showed that the derivatives of cyanidin, peonidin and pelargonidin may be responsible for the pink of mutant petals and S2 stage (buds showing color at the top but with the scales still present) was the key stage of flower color formation of mutant. In total, 412,910 transcripts and 2,780 differentially expressed genes (DEGs) were identified in pairwise comparisons of WT and mutant petals. GO and KEGG enrichment analyses of the DEGs showed that the ‘DNA-binding transcription factor activity’, ‘Flavonoid biosynthesis’ and ‘Phenylpropanoid biosynthesis’ were more active in mutant petals. Early anthocyanin pathway candidate DEGs (CHS3-CHS6, CHI, F3Hs and F3’H) were strongly correlated and up-regulated expression in mutant petals than in WT petals at S2 stage. These genes may be the key structural genes for the pink coloration of mutant petals. In the petals of mutant, two R2R3-MYB unigene (TRINITY_DN59015_c3_g2 and TRINITY_DN49281_c1_g6) were identified as repressors involved in anthocyanin regulation and were significantly down-regulated at S2 stage. This study shed light on the biochemistry and genetic mechanisms underlying the flower coloration in two Rhododendron obtusum cultivars.