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Title: Molecular characterization of an International cocoa collection using microsallte markers

item Zhang, Dapeng
item Mischke, Barbara
item Johnson, Elizabeth
item Meinhardt, Lyndel

Submitted to: Tree Genetics & Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2008
Publication Date: 6/24/2008
Citation: Zhang, D., Mischke, B.S., Johnson, E.S., Mora, A., Phillips-Mora, W., Meinhardt, L.W. 2008. Molecular characterization of an International cocoa collection using microsallte markers. Tree Genetics & Genomics. doi:

Interpretive Summary: Cocoa is an important tropical crop since it is the source of cocoa butter and powder for the confectionery industry. Genetic resources of cocoa are important for breeding new cocoa varieties and thus are of great importance for sustainable cocoa production. Incorrect labeling of the trees and a lack of knowledge regarding their genetic diversity are the main limitations to conservation and to use of cocoa genetic resources. In the present study, we fingerprinted an international collection of cocoa trees maintained in Costa Rica. We identified 140 duplicates in this collection. The evaluation of genetic diversity showed that the trees from South America contributed more of the genetic diversity to this collection than trees from Central America and the Caribbean regions. These results improve our understanding of the genetic diversity that exists in this cocoa collection. These findings will be used by collection curators, plant breeders and cocoa farmers.

Technical Abstract: High levels of redundancy and limited information on genetic structure hinder the efficient conservation and utilization of cacao germplasm. The present study targeted the assessment of genetic identity and population structure in an international cocoa collection maintained in Costa Rica. Using a capillary electrophoresis genotyping system, we fingerprinted 688 Theobroma cacao L. accessions maintained in the CATIE collection. Redundancy within the collection was assessed by comparing a 15 loci SSR profile for each accession. Forty synonymously labeled sets, involving 140 clones were identified. These accounts for 19.6% of the examined accessions in this study. Synonymously labeled sets contained from two to thirty clones which were mainly germplasm introduced from other national collections. Analysis of genetic structure in this collection found that within-group difference account for 84.6% of the total molecular variation whereas the among-group difference accounted for 15.4%. The introduced germplasm from South America contributed more of the among-group variation than those from Central America and Trinidad, as measured by the average genetic distance. The Brazilian germplasm contributed most to this collection in terms of total alleles and private alleles. Principle coordination analysis showed that the Trinitario hybrids from Costa Rica shared a high similarity among groups as well as among individual accessions, which reflects the structure of large groups of sibs or families in these hybrids. The inter-group relationship by cluster analysis largely agreed with the geographical origin of each germplasm group, which substantiated the existing