Transcriptome analysis of floral bud development in <i>Fritillaria pallidiflora</i>

Flowering represents a significant transition from vegetative to reproductive growth, with floral bud development being crucial for the life cycle of ornamental plants. Despite advances in model plants, the molecular regulatory mechanisms governing floral bud development in the perennial ornamental bulbous plant genus <italic>Fritillaria</italic> L remain unclear. In this study, we defined the exact developmental stages of the flower bud of <italic>Fritillaria pallidiflora</italic> and comprehensively analyzed gene expression patterns associated with floral bud development. Based on the morphological observations of paraffin sections, the process of floral bud differentiation in <italic>F. pallidiflora</italic> was classified into six distinct stages: the undifferentiated phase (S0), bract primordium differentiation phase (S1), floral primordium formation phase (S2), petal primordium differentiation phase (S3), stamen primordium differentiation phase (S4), and pistil primordium differentiation phase (S5). Transcriptomic analysis of samples (F1, F2, and F3) from three representative developmental stages (S1, S3, and S5), identified a total of 74,353 unigenes, of which 34,288 were functionally annotated as protein-coding genes. Across the three stages, a total of 3402 differentially expressed genes (DEGs) were identified, among which only nine genes exhibited differential expression consistently at all three stages. GO and KEGG pathway enrichment analyses of the 1886 DEGs revealed that 44 unigenes potentially related to floral bud differentiation were identified, including seven genes associated with circadian rhythm, eight genes involved in carbohydrate metabolism, 11 genes related to plant hormones, seven genes related to temperature, and 11 transcription factors, which can serve as candidate genes for studying floral bud development in <italic>Fritillaria.</italic> Collectively, these findings provide a valuable collection of gene expression patterns that are characteristic of floral bud differentiation in <italic>F. pallidiflora</italic>, which may lay a foundation for dissecting the molecular mechanisms underlying the regulation of flowering time and facilitating molecular breeding in <italic>Fritillaria</italic> species, contributing to elucidation of the molecular mechanisms that regulate floral bud development in other perennial bulbous plants.