SRP492976 PRJNA1083040 Comparative performance of SSR and SNP markers for population analysis in Theobroma cacao to validate a new ddRADseq protocol for cacao genotyping. In order to validate a new ddRADseq protocol for cacao genotyping, 158 cacao plants were genotyped using both an international standard set of 15 SSRs recognized for cacao DNA fingerprint and the ddRADseq protocol abovementioned. Genotypic data were used to compare the performances of both genotyping system for population analysis in cacao, including cacao ancestry analysis.