Genotyping of cocoa trees (Theobroma cacao L.) from first and second cycle of reccurent and reciprocal selection program in Côte d'Ivoire

The recurrent and reciprocal cocoa breeding program in Côte d'Ivoire is in its 2nd cycle of crossing High Amazon Forastero (HA)2 and a mixture of Low Amazon Forastero and Trinitario (LA + T)2. It was created with the aim of improving the characteristics of these genetic groups. This study was carried out to evaluate the identity and genetic structure of cocoa trees selected on index for production and rotted pod rate, with a view to better assessing the genetic conformity of individuals within each genetic group. 152 cocoa trees were genotyped with 99 SNPs markers. These samples included 53 HA2 genotypes, 26 (BA + T)2 genotypes, 30 parents genotypes and 43 progenies from crosses between HA2 and (BA + T)2. Results indicate that observed heterozygosity (Ho = 0.35) is higher than expected heterozygosity (He = 0.31), showing an excess of heterozygotes. Strong genetic differentiation (Fst = 0.90) was revealed between HA2 and (BA + T)2 and weak genetic differentiation between these groups and their offspring (Fst = 0.03). Multivariate analysis revealed two main phylogenetic groups. Group 1 containing almost all HA2 individuals and group 2 comprising almost all (BA + T)2 genotypes. Indeed, genetic conformity of individuals was revealed within each group, with 94% of HA2 genotypes and 81% of (BA + T)2 genotypes. These results are a good indicator for avoiding errors when selecting the best cocoa trees within each genetic group, with a view to starting a new selection cycle.