Assessing Genetic Diversity in Java Fine-Flavor Cocoa (Theobroma cacao L.) Germplasm by Using Simple Sequence Repeat (SSR) Markers

Abstract

Indonesia is the 3 rd largest cocoa-producing country in the world. The cacao varieties currently cultivated in Indonesia are inter-hybrids of various clones introduced from the Americas since the 16th century. Among them, is a well- known fine cocoa specialty product which was originally selected from crosses between Criollo trees and an unknown parent at Djati Roenggo, Java in 1912. Using simple sequence repeat (SSR) markers, we analyzed the genetic diversity and population structure of fine-flavored cacao germplasm from Java, and compared the results with those of bulk cocoa in the same region. Although a high level of heterozygosity was observed in the fine-flavored cacao clones (Ho=0.660; He=0.674), indicating their hybrid origin, the allele richness in the Java cacao germplasm was moderate (7.6 alleles per locus). Principal Coordinate Analysis (PCoA) showed that the genetic structure of Java cocoa is heterogeneous, including genetic background of Trinitario, Upper Amazon and Lower Amazon Forastero. Parentage analysis supported the passport records of parental contribution from Venezuelan landraces to some DR clones (DR 1 and DR 38), which are the main clones used to produce Java cocoa, but excluded the direct parentage of pure Criollo. Sibship reconstruction indicated that the DR clones did not originate from a single cross as previously considered. The resultant information improved our analysis of the diversity and ancestry of Java cocoa. It also suggested the need for broadening the genetic background in the Java cocoa germplasm.