DNA Profiling of Philippine Cacao (Theobroma cacao L.) Varieties Using Microsatellite Markers

Fifteen SSR markers were used to construct a DNA profile of Philippine cacao varieties to assess the genetic similarity, genetic diversity and elucidate relationships between varieties and clones. A total of 50 accessions of cacao were collected, composed of 13 varieties and 7 criollo clones, from 10 provinces in the Philippines. Of the 13 varieties, 6 are National Seed Industry Council (NSIC)-registered. Unweighted pair group method with arithmetic mean (UPGMA) similarity coefficients observed from the cluster analysis of the standard varieties ranged from 0.09 to 0.72, indicating that standard varieties are distinct from one another. The varieties with the highest similarity (72%) were the criollo clones Criollo Green and Criollo Red. At 22% similarity, trinitarios composed the majority in one group. The mixing of other criollos with the trinitario group could be due to their genetic relationship where trinitarios are hybrids between criollo and forastero. All the characterized primers were highly polymorphic with polymorphism information content (PIC) values ranging from 0.6341 to 0.8702. The markers used were repeatable, sufficient and effective in detecting genetic similarities and establishing genetic profiles of the collection.