Temporal Transcriptome Analysis Reveals Core Pathways and Orphan Gene EARLY FLOWERING 1 Regulating Floral Transition in Chinese Cabbage

The floral transition in Chinese cabbage (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) is governed by a complex interplay of gene expression and hormonal regulation. Temporal transcriptome profiling was conducted across three developmental stages: pre-bolting (PBS), bolting (BS), and flowering stages (FS), to investigate the underlying molecular mechanisms. A total of 7092 differentially expressed genes (DEGs) were identified, exhibiting distinct expression trajectories during the transition. Moreover, functional enrichment analyses revealed strong associations with plant hormone signaling, MAPK pathways, and developmental regulation processes. Key flowering-related genes, such as <i>BrFLM</i>, <i>BrAP2</i>, <i>BrFD</i>, <i>BrFT</i>, and <i>BrSOC1s</i> displayed antagonistic expression patterns. Hormonal pathways involving auxin, ABA, ET, BR, GA, JA, CK, and SA showed stage-dependent modulation. Further, orphan genes (OGs), especially <i>EARLY FLOWERING 1</i> (<i>EF1</i>), showed significant upregulation during the transition, which exhibited 1.84-fold and 1.93-fold increases at BS and FS compared to PBS, respectively (<i>p</i> < 0.05). Functional validation through <i>EF1</i> overexpression (EF1OE) in <i>Arabidopsis</i> consistently promoted early flowering. The expression levels of <i>AtFT</i> and <i>AtSOC1</i> were significantly upregulated in EF1OE lines compared to wild-type (WT) plants. The findings contribute to understanding the coordinated genetic and hormonal events driving floral development in Chinese cabbage, suggesting <i>EF1</i> as a candidate for bolting resistance breeding. This work also expands the existing regulatory framework through the successful integration of OGs into the complex floral induction system of <i>Brassica</i> crops.