Temporal Shifts in Hormone Signaling Networks Orchestrate Soybean Floral Development Under Field Conditions: An RNA-Seq Study

Floral ontogeny in soybean (<i>Glycine max</i>) is governed by multilayered regulatory hierarchies that integrate phytohormonal cues with precisely choreographed gene-expression programs. Yet, the transcriptomic architecture underpinning this continuum remains only partially resolved. Here, we generated a strand-specific, high-depth temporal transcriptome atlas of soybean inflorescences spanning four morphologically defined stadiums (Stadium 0-Stadium 3). We detected transcriptional activity for 60,889 loci; pairwise stadium contrasts revealed 4000-7000 differentially expressed genes, with the most extensive reprogramming coinciding with the onset of anthesis (Stadium 2). Unsupervised clustering delineated ~600 genes peaking at the pre-anthesis phase (Stadium 1), a cohort enriched for transcriptional regulators and floral organ-identity determinants. Stadium-resolved gene-set enrichment and KEGG mapping uncovered dynamic modulation of canonical hormone-signaling pathways-including auxin, cytokinin, gibberellin, abscisic acid, ethylene, jasmonate, and salicylate circuits-reflecting shifting developmental priorities. Forty-five MADS-box transcription factor genes were expressed; notably, <i>JOINTLESS</i> was strongly induced at anthesis, while the root-predominant factor <i>GmNMH7</i> exhibited unexpected floral expression, implicating a hitherto unappreciated role in reproductive development. Quantitative RT-PCR of representative loci corroborated RNA-seq measurements. This high-resolution atlas refines our understanding of the hormonal and genetic circuitry of soybean floral morphogenesis, furnishing molecular targets for engineering flowering time and inflorescence architecture under fluctuating environmental conditions.