Integrated multi-omics and WGCNA analyses reveal pathways and candidate genes associated with branching flower development in Nymphaea prolifera: focusing on hormone homeostasis and flavonoid biosynthesis

BACKGROUND: Nymphaea prolifera employs a unique asexual reproductive strategy in which its normal flowers transform into branching flowers. These are specialized structures that develop vegetative propagules. These propagules can directly sprout into new plants. As the branching flowers mature, they detach from the parent plant and form new, independent individuals. However, the underlying molecular mechanisms that govern this distinctive reproductive phenomenon remain unclear. RESULTS: In this study, microscopic observations were conducted on normal flowers and branching flowers of Nymphaea prolifera. The results showed that reproductive organ tissues such as the pistils (including ovaries and ovules) of branching flowers were completely transdifferentiated into vegetative propagules, which could continuously generate multiple generations of branching flowers. Analyses of endogenous hormones, transcriptomes, and metabolomes were performed on branching flowers at four developmental stages (bud stage, early flowering stage, middle flowering stage, and late flowering stage) as well as on normal flowers. The results revealed significant differences in eight hormone compounds between branching flowers and normal flowers, including 2 cytokinins, 4 auxin-related compounds, ABA, and GA₄. GO and KEGG functional enrichment analyses indicated that both differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were significantly enriched in the flavonoid biosynthesis pathway. Furthermore, the expression levels of genes and metabolites associated with this pathway were gradually up-regulated during the development of branching flowers. Weighted gene co-expression network analysis (WGCNA) identified three core modules (MEgreen, MEblue, MEturquoise) that were highly correlated with hormone and flavonoid metabolism, and screened out potential candidate genes IAA17, ARF6, ABF1 that may be associated with endogenous hormone and flavonoid metabolism. CONCLUSIONS: This study reveals the morphological and molecular characteristics of branching flower development in N. prolifera. It identifies the hub genes, modules and metabolic pathways involved in this phenomenon, thereby providing a comprehensive morphological and molecular basis for elucidating this species' unique asexual reproductive mechanism.