Molecular markers were generated from the completed DOST-PCAARRD funded project to identify National Seed Industry Council (NSIC) recommended cacao varieties, true Criollo types and cacao accessions with resistance to cacao vascular streak disease caused by Lasiodiplodia theobroma and cacao pod rot disease caused by Phytophtora palmivora. There is a need to validate these markers for utility in the identification of authentic cacao varieties and Criollos and in marker-assisted selection/breeding. The study aims to validate SSR markers to identify NSIC recommended cacao varieties in commercial nurseries; to assess the claimed Criollo cacao types in the Philippines for identification of authentic or true-to-type Criollos, and to validate the SSR markers for identification of cacao breeding materials with resistance to cacao vascular streak disease and pod rot diseases. The Bureau of Plant Industry and accredited cacao nurseries in Regions XI and XII were communicated for collaboration and implementation of the project. Leaf samples were collected for DNA extraction, PCR amplification and fingerprint analysis using the primers of identified SSR markers. Samples were randomly collected with 5-10 plants per variety in the nurseries. A total of 555 leaf samples of cacao seedlings from 39 nurseries across Regions XI and XII consist of 293 UF18 and 262 BR25 were collected and validated. Moreover, 201 claimed-Criollo, five (5) Forastero, and six (6) Trinitario collected from different regions in the Philippines were molecularly analyzed using the 22 SSR markers. Cluster analysis revealed similarity coefficients ranging from 0.35 to 100 with clusters indicating Criollo, Trinitario and Forastero. In addition, cluster analysis showed putative true Criollo types from 0.51 to 100 coefficients, which needed further evaluation at phenotypic and genomic levels. Furthermore, 21 cacao accessions from the University of Southern Mindanao genebank were collected and molecularly screened for disease resistance. SSR markers C10238t1 and C1618t2 were used for screening of samples for resistance to cacao pod rot disease caused by P. palmivora; and markers C4101t2, CDRAat11 P3T7 C74 and C1223t3 were used for screening of samples for resistance to vascular streak disease caused by L. theobromae.
