Molecular mechanism of flower color formation in Rhododendron simsii Planchon revealed by integration of microRNAome and RNAomics

Abstract Background Systems-wide understanding of gene regulatory networks underlying flower color formation in Rhododendron simsii is insufficient. In this research, integration analysis of microRNAome and RNAomics were performed to reveal the molecular mechanism of flower color formation in three R. simsii varieties with red, pink, and crimson flowers, respectively. Results A total of 213 miRNAs, containing 151 known miRNAs belonging to 55 families and 62 novel miRNA, were identified. In particular, 53 miRNAs were significantly differently expressed. The top significant enriched GO terms were mainly “meristem maintenance”, “carbohydrate metabolic process”, and “signal transduction”. The main KEGG pathways were “Monobactam biosynthesis”, “Plant-pathogen interaction”, and “MAPK signaling pathway-plant”. The miRNA–mRNA regulatory network construction showed that key genes and pathways were mainly associated with synthesis of secondary metabolites. In particular, ath-miR5658 could affect the synthesis of pelargonidin, cyanidin, and delphinidin through downregulating expression of anthocyanidin 3-O-glucosyltransferase; ath-miR868-3p could regulate isoflavonoid biosynthesis through downregulating expression of CYP81E1/E7; ath-miR156g regulated the expression of flavonoid 3',5'-hydroxylase; ath-miR829-5p regulated flavonol synthase in flavonoid biosynthesis process. Conclusion This research will provide critical clues of flower color formation, and provide novel insights into the breeding of new varieties with rich flower color.