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Elucidation of genetic identity and population structure of cacao germplasm within an international cacao genebank

Published online by Cambridge University Press:  23 October 2012

Lambert A. Motilal ,
Dapeng Zhang ,
Pathmanathan Umaharan ,
Michel Boccara ,
Sue Mischke ,
Antoinette Sankar  and
Lyndel W. Meinhardt
Lambert A. Motilal*
Affiliation:
Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, Republic of Trinidad and Tobago, West Indies
Dapeng Zhang
Affiliation:
USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD20705, USA
Pathmanathan Umaharan
Affiliation:
Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, Republic of Trinidad and Tobago, West Indies
Michel Boccara
Affiliation:
Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, Republic of Trinidad and Tobago, West Indies Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Biological Systems Department, Unité Mixte de Recherche Développement et Amélioration des Plantes (UMR DAP) TA A 96/03-34,398, Montpellier, France
Sue Mischke
Affiliation:
USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD20705, USA
Antoinette Sankar
Affiliation:
Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, Republic of Trinidad and Tobago, West Indies
Lyndel W. Meinhardt
Affiliation:
USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD20705, USA
*
*Corresponding author. E-mail: [email protected]
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Abstract

Theobroma cacao L., or cacao, is the source of cocoa products used in the making of chocolate. These tropical trees are conserved in living genebanks. The International Cocoa Genebank, Trinidad is one of the largest ex situ collections in the public domain. Mislabelling is a critical problem and the correction of this problem is vital to improve the accuracy and efficiency of genebank management. Using microsatellite DNA markers, we assessed the level of mislabelling in a group of Refractario cacao that originated from Ecuador and determined their population memberships through Bayesian clustering analysis. The microsatellite data revealed a synonymous rate of 7.5% and an error rate of 39.4% in this germplasm subset. The analysis of the population structure grouped the Refractario accessions into four subclusters, indicating intra-population heterogeneity in this germplasm group. Based on the results, we recommend that when the assignment test is used for cacao genotype identification, it should (a) use duplicated samples as internal checks, (b) choose suitable reference accessions, including a known homogeneous group and (c) employ subclustering checks to obtain reliable results. The information framework generated is discussed in relation to the management of the collection, population enhancement and future research of the collection.

Keywords

cocoaconservationfield genebankmislabellingpopulation structuretree identity
Type
Research Article
Information
Plant Genetic Resources , Volume 10 , Issue 3 , December 2012 , pp. 232 - 241
Copyright
Copyright © NIAB 2012

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