Assessing genetic diversity in java fine-flavor cocoa (theobroma cacao l.) Germplasm by simple sequence repeat (ssr) markers

Authors: SUSILO, AGUNG - Indonesian Coffee And Cocoa Research Institute; Zhang, Dapeng; MOTALAL, LAMBERT - University Of The West Indies; Meinhardt, Lyndel

Submitted to: Tropical Agriculture (Trinidad)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/14/2011
Publication Date: 6/10/2011
Citation: Susilo, A., Zhang, D., Motalal, L., Meinhardt, L.W. 2011. Assessing genetic diversity in java fine-flavor cocoa (theobroma cacao l.) Germplasm by simple sequence repeat (ssr) markers. Tropical Agriculture (Trinidad). 55:84-92.

Interpretive Summary: Cacao is an important tropical tree crop since it is the source of cocoa butter and powder for the confectionery and chocolate industries. Genetic resources of cacao are important for breeding new cacao varieties and thus are of great importance for sustainable cacao production. Indonesia is the 3rd largest cocoa producing countries in the world. The currently cultivated cacao varieties in Indonesia were inter-hybrids of various clones introduced from the Americas since the 16th century. Among them, Java cocoa is a well-known fine cocoa specialty product. Using DNA fingerprinting technology, we analyzed the genetic diversity in the fine-flavor cacao varieties from Java, and compared the results with those of bulk cocoa in the same region. The result supports the passport records of parental contribution from Venezuelan landraces, but there was no direct parentage contribution from Criollo cacao. It also shows that there is limited genetic diversity in the Java Cocoa, suggesting the need to broaden the genetic background in the Java cocoa germplasm. These results improve our understanding of the genetic diversity in the Indonesian cacao germplasm and will improve the breeding of better cacao varieties in this region. These results will be useful to plant breeders, germplasm curators and cacao farmers and will benefit chocolate consumers.

Technical Abstract: Indonesia is the 3rd largest cocoa producing countries in the world, with an annual cacao bean production of 572,000 tons. The currently cultivated cacao varieties in Indonesia were inter-hybrids of various clones introduced from the Americas since the 16th century. Among them, “Java cocoa” is a well-known fine cocoa specialty product which was originally selected from crosses between “Java 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 flavor cacao germplasm from Java, and compared the results with those of bulk cocoa in the same region. A high level of heterozygosity was observed in the fine flavor cacao clones (Ho=0.660; He=0.674), indicating their hybrid origin, but the allele richness in the Java cacao germplasm was moderate (7.6 allele per loci). The genetic distance between the fine cocoa and bulk cacao is negligible (Nei’s distance=0.057), indicating that the two groups shared a common genetic origin. Principal Coordinate Analysis (PCoA) shows that the Java cocoa is heterogeneous in genetic structure, including genetic background of Trinitario, Upper Amazon and Lower Amazon Forastero. Parentage analysis supports the passport records of parental contribution from Venezuelan landraces to some DR clones (DR 1 and DR 38), but excluded the direct parentage of Criollo. Sibship reconstruction indicates that the DR clones were not from a single cross as people believed. The resultant information improved our understanding of the diversity and ancestry of Java cocoa. It also suggests that there is a need to broaden the genetic background in the Java cocoa germplasm, with resistance to Cacao pod borer (Conopomorpha cramerella), Vascular streak dieback (Oncobasidium theobromae) and Root-rot disease (Fomes lamaoensis).