Transcriptional footprints associated with bud fertility in grapevine development (Vitis vinifera L.)

Abstract Main conclusion Transcriptomic analyses carried out on buds at different positions and developmental stages reveal the functional domains mainly involved in determining bud fertility in grapevine, with a focus on hormone signalling and floral integrators. Abstract Bud fruitfulness in grapevine ( Vitis vinifera L.) depends on complex interactions between developmental stage, node position and hormonal regulation. In this study, transcriptomic analyses were performed on buds of cv. Merlot collected at three phenological stages (BBCH63, BBCH77 and BBCH90) from three node positions (2, 5 and 10), representing basal, intermediate and apical fertility patterns. RNA-Seq data revealed that phenological stage was the primary driver of transcriptional variation, while node position contributed to intra-stage differences. BBCH77 emerged as the most transcriptionally dynamic phase. Differential expression, enrichment analyses and WGCNA highlighted distinct developmental trajectories among nodes. Buds at node 5, characterized by lower fertility, showed transcriptional signatures associated with enhanced gibberellin biosynthesis and signalling, early activation of dormancy-related pathways, and complex hormonal interplay involving ethylene. In contrast, buds at node 10 displayed transcriptional features consistent with sustained auxin flux from the shoot apical meristem and reduced local inhibitory signalling, potentially supporting higher fertility. Cytokinin-related genes showed stage-dependent activation, particularly at BBCH77, suggesting a transient promotive role during floral transition. Expression profiling of flowering-related genes confirmed stage-dependent regulation of major floral integrators and revealed position-specific modulation of key regulators. Overall, the integration of positional and temporal transcriptomics supports a working model in which bud fertility results from the dynamic balance between stimulatory (auxin, cytokinins) and inhibitory (gibberellins, ethylene, ABA) signals, modulated by developmental stage and meristem proximity.