Towards the Identification of Candidate Genes Linked to the “Arriba Flavor” in “Nacional” Ecuadorian Cacao: Methodological Approach and Advances

There are two categories of quality recognized by the world market of cocoa beans: the “standard quality cocoa”, which corresponds to 95% of the total market; and the “fine flavored cocoa” which is mainly produced by the Criollo and Nacional varieties, and brings a higher price in the market. Ecuador’s fine-flavored cacao or “Nacional cacao” is a native material which is recognized worldwide because of its aromatic and flavor known as “sabor arriba”. This project aims to identify candidate genes linked to the Arriba flavor by applying an analysis of the transcriptome in INIAP commercial clones (EET) which come from a rigorous selection process of fine-flavored landraces in Ecuador. For this purpose RNAseq analysis was conducted in self-pollinated beans of EET clones in different states of development. For each genotype RNA was extracted from a pool of beans after 18, 20, and 22 weeks, and after 24 and 48 hours of microfermentation. cDNA libraries obtained for each genotype/condition are then sequenced by ILLUMINA technology and the bioinformatics analysis are compared with the Criollo reference genome and the transcriptome which are available. The experimental and bioinformatic approaches that are being used for identifying candidate genes potentially linked to National quality will be presented, as well as the partial results of the differential gene expression analysis with one of the sequenced clones.