Genotyping of Cocoa Trees (Theobroma cacao L.) from the First and Second Cycles of the Recurrent and Reciprocal Selection Program in Côte d'Ivoire

The recurrent and reciprocal cocoa breeding program in C & ocirc;te d'Ivoire is in its 2nd cycle of crossing Upper Amazonian Forastero (HA)2 and a mixture of Lower Amazonian Forastero and Trinitario (BA + 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 diversity and structure of cocoa trees selected via index for production and the rate of pod rot to better assess the genetic conformity of individuals within each genetic group. A total of 152 cocoa trees were genotyped with 99 SNP markers polymorphs. These samples included 53 HA2 genotypes, 26 (BA + T)2 genotypes, 30 parental genotypes and 43 progenies from crosses between HA2 and (BA + T)2. The results indicate that the observed heterozygosity (Ho = 0.35) is greater than the expected heterozygosity (He = 0.31), indicating an excess of heterozygotes. Strong genetic differentiation (F-ST = 0.90) was revealed between HA2 and (BA + T)2, and weak genetic differentiation was observed between these groups and their offspring (F-ST = 0.03). Multivariate analysis revealed two main phylogenetic groups. Group 1 contained almost all the HA2 individuals, and Group 2 contained almost all the (BA + T)2 genotypes. Indeed, genetic conformity of individuals was revealed within each group, with 94% presenting HA2 genotypes and 81% presenting (BA + T)2 genotypes. These results are good indicators for selecting the best cocoa trees within each genetic group, with the goal of starting a new selection cycle.