Transcriptome analysis and hormone metabolic profiling provide molecular insights into flowering process in petunia

The flowering process is a complex biological event regulated by coordinated transcriptional programs and hormone signaling. Petunia hybrida is an important ornamental plant, yet the integrative regulatory mechanisms between hormones and gene expression during flowering remain poorly understood. In this study, flowers of the petunia cultivar ‘112’ were classified into three developmental stages based on days before anthesis: 7 days before flowering (DBF7), 4 days before flowering (DBF4), and the day of flowering (F). Integrated transcriptomic and hormone profiling analyses were conducted to systematically investigate gene expression dynamics and hormone metabolism during the flowering process. High-quality RNA sequencing generated over 483.36 million clean reads, with mapping rates exceeding 83.9% against the petunia reference genome. Comparative transcriptome analysis identified 7,160, 8,687, and 11,161 differentially expressed genes (DEGs) in DBF4 vs. DBF7, F vs. DBF4, and F vs. DBF7, respectively. K-means clustering divided DEGs into four expression modules associated with primary metabolism, secondary metabolite biosynthesis, hormone signal transduction, and floral organ morphogenesis. Transcription factor analysis revealed that bHLH, bZIP, MADS, TCP, and WRKY families exhibited distinct stage-specific expression patterns during the flowering process. Hormone profiling revealed dynamic changes in auxin, gibberellin, jasmonate, salicylic acid, and abscisic acid contents. Integrated transcriptomic and hormone analyses showed that auxin, gibberellin, and jasmonate biosynthesis pathways were predominantly active during early developmental stages, in accordance with the expression dynamics of major biosynthetic genes ( PhYUC , PhTAR , PhGA20ox , PhGA3ox , PhLOX , PhAOS , and PhOPR3 ). Gene–hormone network analysis revealed interconnections among phytohormone signaling pathways, particularly between jasmonate–gibberellin and abscisic acid–cytokinin, which are associated with representative genes involved in jasmonate-related lipid metabolism ( PhPLA2A and PhOPR11 ), phenylpropanoid metabolism ( PhPAL1 and PhCAMT3 ), and cell wall modification ( PhPGLR4 and PhGUN25 ) during the flowering process. This study provides a comprehensive overview of the transcriptional and hormonal regulatory networks governing the flowering process in petunia. Our results reveal a stage-specific regulatory framework in which coordinated gene expression and phytohormone interactions contribute to flower development and opening, providing potential genetic resources for the improvement of ornamental traits in petunia.