With showy display and multi-color, Iris germanica (Bearded iris) is one of the most popular ornamental perennials, of which molecular mechanisms in regulation of flowering are poorly understood. The objectives of this study were to reveal profiles of endogenous phytohormones and identify critical genes in floral regulation during flower development. The development process of flowering from initiation of inflorescence to flower stem elongation was observed. Based on the observation results, plant materials at four critical development stages were collected to identify the endogenous phytochromes and genes regulating flowering by using high performance liquid chromatography (HPLC) and high-throughput RNA sequencing. The concentration of different endogenous phytohormones showed various trends at four stages. Among identified phytohormones, the concentrations of Indole-3-acetic acid (IAA) and abscisic acid (ABA) were relatively high when compared with the active forms of other phytohormones. Besides, the concentration of IAA was low at pistil and petal primordium stage under winter low temperature conditions and increased at petal and stem elongation stages, while the concentration changes of ABA showed opposite trend. With comprehensive analysis of the DEGs annotated with the GO, KEGG and NR databases, homologs of critical genes in flowering regulatory pathway, such as IgAP2, IgFRI, IgSVP, IgVIN3-1, IgVIN3-2, IgGI et al. were identified. Correlation analysis between DEGs and phytohormones showed that IgFLC, IgFRI, IgVIN3-1 had closely negative relations with IAA and positive relations with ABA. The result indicates that IgFLC, IgFRI and IgVIN3-1 might be key genes in regulation of the flowering process during the flower bud development. The profiles of endogenous phytohormones and critical flowering genes identified in this study could provide references for further research on regulation of flower time in I. germanica or other species in this genus.
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