“Refractario” cocoa – genetic identity and genetic structure assessed using microsallite markers

Authors: Zhang, Dapeng; BOCCARA, MICHEL - UNIV OF WEST INDIES; MOTILAL, LAMBERT - UNIV OF WEST INDIES; BUTLER, DAVID - UNIV OF WEST INDIES; UMAHARAN, PATHMANATHAN - UNIV OF WEST INDIES; Mischke, Barbara; Meinhardt, Lyndel

Submitted to: Conservation Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/8/2006
Publication Date: 6/5/2006
Citation: Zhang, D., Boccara, M., Motilal, L., Butler, D.R., Umaharan, P., Mischke, B.S., Meinhardt, L.W. 2006. “Refractario” cocoa – genetic identity and genetic structure assessed using microsallite markers. Conservation Genetics. 9(2):327-337.

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 trees in collections and a lack of knowledge about their genetic diversity limit the conservation and use of these cocoa genetic resources. In the present study, we assessed the individual identity, family membership and population structures of "Refractario" cocoa, a population of trees collected in Ecuador in the 1930's. A total of 135 mislabeled varieties were identified by comparing their DNA fingerprints. Genetic analysis showed that the "Refractario" cocoa trees have unique genetic profiles. These results improve our understanding of how to identify and manage duplicated and mislabeled trees and provide important genetic diversity information. This information will contribute to a more efficient management of cocoa germplasm and will improve the breeding of better cocoa varieties. These results will be useful to plant breeders, germplasm curators and cocoa farmers and will benefit chocolate consumers.

Technical Abstract: The utilization of germplasm for crop improvement is often hampered by the absence of detailed information regarding the origin, genetic identity and genealogical relationship of germplasm groups or populations. The majority of cacao germplasm held in the Universal Collection of the International Cocoa Genebank, Trinidad was collected in the 1930s’ and the passport data were either incomplete or had many ambiguities. Molecular marker technology offers a highly efficient tool to verify the existing passport data and reconstruct the missing information. In the present study, we assessed the individual identity, family membership and population structures in the “Refractario” cacao, a group of germplasm collected in Ecuador. Using a high-throughput genotyping system with 15 microsatellite loci, we fingerprinted 483 accessions in 48 half-sib families collected from nine farms. Based on the multi-locus profiles, a Bayesian method for individual assignment was applied to verify the membership in each half-sib family. A total of 135 mislabelled accessions were identified by the assignment test. Principal coordinate and cluster analyses showed that the genetic profile of the Refractario cacao was different from the other germplasm groups, except the Nacional cocoa from the coastal valley of Ecuador. Partitioning of the genetic variation in the Refractario group showed that majority of the variation (86%) was contributed by within-farm differentiation. The inter-farm variation accounted for 14% of the total variance and was highly significant. Results of cluster analysis and principle coordinate analysis showed a population sub-structure in the Refractario group. The Refractario group was also highly heterozygous, suggesting it may be a hybrid derived from the Nacional cocoa and multiple other parental varieties. However, these possible parental varieties all shared a similar genetic background. The improved understanding of the identities and structure in the Refractario cacao will contribute to a more efficient conservation and use of this germplasm group in cacao breeding.