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AOBPreview originally published online on July 15, 2006
Annals of Botany 2006 98(3):647-655; doi:10.1093/aob/mcl146
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© 2006 The Author(s)

Genetic Diversity and Structure of Managed and Semi-natural Populations of Cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru

DAPENG ZHANG1,*, ENRIQUE AREVALO-GARDINI2, SUE MISCHKE1, LUIS ZÚÑIGA-CERNADES2, ALEJANDRO BARRETO-CHAVEZ2 and JORGE ADRIAZOLA DEL AGUILA2

1 USDA ARS PSI SPCL, 10300 Baltimore Avenue, Bldg 050, Rm 100, BARC-W, Beltsville, MD 20705, USA and 2 Intituto de Cultivos Tropiocales (ICT), Jr Santa Maria, 241, Banda del Shilcayo, Tarapoto, Peru

* For correspondence. E-mail ZhangD{at}ba.ars.usda.gov

Received: 31 December 2005    Returned for revision: 11 April 2006    Accepted: 30 May 2006    Published electronically: 15 July 2006

• Background and Aims Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population.

•Methods Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations.

•Key Results Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests.

•Conclusions These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.

Key words: Theobroma cacao, cocoa, conservation, germplasm, DNA fingerprinting, genetic diversity, population structure, Peru, Huallaga, Ucayali


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