The cultivation of cacao represents an income option and a source of employment for thousands of small producers in Central America. In Honduras, due to the demand for fine flavor cacao to produce high-quality chocolate, the number of hectares planted is increasing. In addition, cacao clones belonging to the genetic group named Criollo are in great demand since their white beans lack of bitterness and excellent aroma are used in the manufacturing of premium chocolate. Unfortunately, the low resistance to pests and diseases and less productive potential of Criollo cacao leads to the replacement with vigorous new cultivars belonging to the other genetic groups or admixture of them. In this study, 89 samples showing phenotypic traits of Criollo cacao from four regions of Honduras (Copán, Santa Bárbara, Intibucá, and Olancho) were selected to study their genetic purity using 16 SSR molecular markers. The results showed that some samples belong to the Criollo group while other accessions have genetic characteristics of “Trinitario” or other admixtures cacao types. These results confirm the genetic purity of Criollo cacao in Honduras, reaffirming the theory that Mesoamerica is a cacao domestication center and also serves to generate interest in the conservation of this genetic wealth both in-situ and ex-situ.

The molecular pathways underlying floral activation and development are well described in model species, but exhibit significant diversity in plants that is poorly understood in crops with complex cycles, such as Coffea arabica L. The reproductive development of coffee plants is biannual, and the flowering time is crucial for the coffee productivity and cup quality. In this study, we explored the plasticity of floral development and flowering-time of contrasting coffee genotypes to understand the associated metabolic and regulatory transcriptional profiles. Firstly, we compared the reproductive development of three coffee genotypes, confirming that Acauã is late flowering, Oeiras is early flowering, and the natural mutant Semperflorens ( Sf ) exhibits continuous flowering throughout the year. Analysis of sugar and ethylene content revealed quantitative differences between genotypes in both leaves and floral buds. To associate these phenotypic differences with the regulatory developmental pathways, we performed RNA-seq analysis comparing the shoot apical meristems, floral buds and leaves of different genotypes. Our analysis identified 12.478 differentially expressed genes, which showed enriched terms mainly related to hormonal regulation, external stimulus and floral development. Notably, some major players of reproductive development, as homologs of FLOWERING LOCUS T and MADS-box genes, showed contrasting expression patterns, generally being ectopically upregulated in the Sf mutant. These findings were associated with the phenotypic differences among coffee genotypes. In conclusion, the present study improves the understanding of the divergence of floral development in coffee, providing valuable insights for directing breeding programs and future studies aiming at controlling floral development and enhancing crop production.