Genetic classification of Vietnamese cacao cultivars assessed by SNP and SSR markers

Vietnam has the potential to become a larger cocoa producer as the country experiences climatic conditions favorable to the growth of the crop. However, to enable a high cacao quality, genetic methods are required to identify and conserve promising cacao cultivars. Previous research as discussed by Everaert et al. (2017), using 14 microsatellite (SSR) markers, showed a genetic characterization of Vietnamese cacao, but additional research is required to further clarify the genetic background of the different Vietnamese cacao cultivars. Therefore, in this study, the Vietnamese dataset was enlarged, and a classification model was developed. Firstly, we compared the classification strength of the 14 previously applied SSR markers and 42 additional single nucleotide polymorphism (SNP) markers, either separately or combined, using 53 international reference cacao cultivars. Secondly, the most classifying marker set was used to examine the genetic associations of the Vietnamese cultivars to the reference cultivars, using Bayesian clustering and principal coordinate analysis (PCoA). The classification method based on the combined marker set performed best and could subdivide the Vietnamese cultivars in three clusters. The first cluster was strongly related to Nanay, the second to Criollo/Trinitario, and the third predominantly to Amelonado and Criollo/Trinitario. For all marker sets, an apparent high genetic diversity could be observed for the total Vietnam collection. The obtained knowledge provides a strong genetic basis for the Vietnamese cacao industry. In addition, the proposed marker set and the analysis workflow could be applied worldwide for future breeding programs and further production of origin chocolate.