Key regulators of floral induction in faba bean (Vicia faba L.) are revealed from spatio-temporal gene expression analysis of contrasting genotypes

Flowering time is a crucial trait for crop adaptation and yield stability, yet its genetic regulation in Vicia faba remains poorly understood. In this study, we performed RNA-sequencing of shoot apex (SA) and leaf tissues to investigate the genetic mechanisms underlying variation in flowering time between two contrasting cultivars, Gubbestad (early flowering) and Honey (late flowering). Based on differential gene expression analysis, K-means clustering and weighted gene co-expression network analysis (WGCNA), we identified key transcriptional modules enriched in genes associated with gibberellin (GA) signaling, photoperiod response, and floral induction. Notably, FT homologs exhibited distinct expression patterns: two FT genes were expressed in Gubbestad, whereas only one was detected in Honey, in the SA during the reproductive stage. The late-flowering cultivar displayed high expression of the transcriptional cofactor TFL1 and transcription factor AP2 in the SA at the vegetative stage, which likely contributed to late floral initiation by suppressing downstream activators of flowering such as SOC1, AP1, and SPL/miR156. In contrast, the early-flowering cultivar showed FT gene expression in both leaf and SA, promoting LFY, SOC1 which accelerate floral transition. Through co-expression analysis, WGCNA identified SOC1 and AG as key hub genes within flowering-related modules, co-expressed with multiple genes encoding regulators of floral development. Our findings highlight the interplay between GA-mediated flowering pathways and photoperiod-responsive genes, revealing a complex regulatory network that controls floral induction. Unraveling these molecular mechanisms provides insights into breeding faba bean cultivars that are better adapted to different geographical regions.