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

Abstract

Systems-wide understanding of gene expression profile regulating flower color formation in Rhododendron simsii Planchon is insufficient. In this research, integration analysis of RNAomics and microRNAome were performed to reveal the molecular mechanism of flower color formation in three R. simsii varieties with red, pink, and crimson flowers, respectively. Totally, 3,129, 5,755, and 5,295 DEGs were identified through comparative transcriptome analysis between ‘Red variety’ and ‘Pink variety’ (1,507 up-regulated and 1,622 down-regulated), ‘Red variety’ and ‘Crimson variety’ (2,148 up-regulated 3,607 down-regulated), as well as ‘Pink variety’ and ‘Crimson variety’ (2,089 up-regulated and 3,206 down-regulated), which were involved in processes of “catalytic activity”, “binding”, “metabolic process”, and “cellular process”, as well as pathways of “metabolic pathways”, “biosynthesis of secondary metabolites”, “plant-pathogen interaction”, and “phenylpropanoid biosynthesis”. A total of 215 miRNAs, containing 153 known miRNAs belonging to 57 families and 62 novel miRNA, were involving in flower color formation. In particular, 55 miRNAs were significantly differently expressed. Based on miRNA–mRNA regulatory network, ath-miR5658 could affect the synthesis of pelargonidin, cyanidin, and delphinidin through downregulating accumulation 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; and ath-miR829-5p regulated flavonol synthasein flavonoid biosynthesis process. This research will provide important roles in breeding new varieties with rich flower color.