Abstract
Theobroma cacao is a tree native to the Latin America humid tropical regions. It is cultivated for its beans, which are used to produce chocolate. The Nacional variety, native to Ecuador, is a fine cocoa variety known for its floral and spicy aromas, called "Arriba" flavour. The genetic and biochemical determinants of the development of its flavours remain poorly understood. The work of this thesis focused on the study of the genetic and biochemical determinants of the aromas of Ecuadorian fine cocoa in order to contribute to the knowledge in this area.The first part of the study was carried out using a population of modern Nacional cocoa trees, which is the variety of Nacional currently grown in Ecuador. Association studies were carried out on the whole genome and focused on the analysis of volatile compounds related to floral and fruity aromas (fresh and dried fruits) contained in the beans before and after roasting, as well as on the results of sensory analyses of liquors. This first study showed that the floral aromas of Nacional were mainly synthesized through two biosynthetic pathways: the monoterpene biosynthetic and the L-phenylalanine degradation pathways. The results related to fruity flavours highlighted five major metabolic pathways: the monoterpene biosynthetic pathway, the degradation of L-phenylalanine, sugars, fatty acids and proteins pathways. Candidate genes encoding enzymes involved in these metabolic pathways were identified in the corresponding association areas.The modern Nacional variety is the result of several generations of crosses between Trinitarios (hybrids between Amelonado and Criollo) and the ancestral Nacional, so, involving three contracted ancestors. The effect of this recent domestication stage on the aromas of the modern Nacional variety was studied. Using genotyping data from the 3 reference ancestors and GWAS results for all quality traits (volatile and non-volatile compounds, sensory analysis); it was possible to determine the origin of the alleles with a positive effect on aroma in the different association areas. This study showed that all founders contributed alleles favourable to the synthesis of quality aromas (floral, fruity ...) but also to the synthesis of defects (bitterness, astringency…). We were able to show that the association zones linked to favourable aromas and those linked to defects were not genetically linked. It is therefore possible to select the areas of interest for the flavours while counter-selecting the areas that bring defects.The second part of this study focused on the analysis of the flavours of a population of cocoa trees native to Amazonia, and to the area of origin of the Nacional ancestral variety. In this study, GWAS analyses were also performed on all the quality traits analysed previously. Ninety seven candidate genes, are common to both populations analysed. New volatile compounds and new association zones were also detected, showing the greater diversity and aromatic richness of these new genetic resources and their interest in the creation of new aromatic varieties adapted to the Amazon.Finally, a GWAS study on non-volatile compounds, sensory traits linked to bitterness and astringency, as well as fat and protein contents, was also carried out on the two populations. Candidate genes linked to the caffeine biosynthetic pathway and that of polyphenols, or linked to the fatty acid biosynthesis pathway have been observed in the association areas.