Exploring the Molecular Pathways of Coffee Flowering Time: A Comparative Analysis of the Semperflorens Mutant and Contrasting Elite Genotypes

Abstract The molecular pathways underlying floral activation and development are well described in model species but exhibit significant diversity in socioeconomically important crops with complex cycles, such as Coffea arabica L. The reproductive development of coffee plants is biennial, and the flowering time is crucial for coffee productivity and cup quality. This study explored the plasticity of floral development and flowering time in three contrasting coffee genotypes to elucidate the associated metabolic and transcriptional regulatory profiles. Firstly, we compared the reproductive development of three coffee genotypes, confirming that Acauã is a late-flowering genotype, whereas Oeiras is an early-flowering genotype, and the natural mutant Semperflorens ( Sf ) exhibits continuous flowering throughout the year. Then, sugar and ethylene content analysis revealed quantitative differences between genotypes in both leaves and floral buds. To associate these phenotypic differences with regulatory developmental pathways, we performed RNA-seq analysis comparing shoot apical meristems, floral buds, and leaves from different genotypes. From this, we identified 12,478 differentially expressed genes, which showed enrichment for gene ontology terms mainly related to hormonal regulation, external stimuli, and floral development. Interestingly, differences among coffee genotypes appeared to be related to ethylene- and auxin-related pathways. Moreover, some major players of reproductive development, such as homologs of FLOWERING LOCUS T and MADS-box genes, showed contrasting expression patterns, generally being ectopically upregulated in the Sf mutant. These findings correlate to the phenotypic differences observed among coffee genotypes. Overall, this study advances our understanding of floral development and plasticity in coffee, providing valuable insights to guide breeding programs and future research focused on regulating floral development and improving crop productivity.