title: Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru.
abstract: OBJECTIVE
  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.
  
  
  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.
authors.affiliation: USDA ARS PSI SPCL, 10300 Baltimore Avenue, Bldg 050, Rm 100, BARC-W, Beltsville, MD 20705, USA. ZhangD@ba.ars.usda.gov
authors.forename: Dapeng
authors.initials: D
authors.lastname: Zhang
authors.forename: Enrique
authors.initials: E
authors.lastname: Arevalo-Gardini
authors.forename: Sue
authors.initials: S
authors.lastname: Mischke
authors.forename: Luis
authors.initials: L
authors.lastname: Zúñiga-Cernades
authors.forename: Alejandro
authors.initials: A
authors.lastname: Barreto-Chavez
authors.forename: Jorge Adriazola
authors.initials: JA
authors.lastname: Del Aguila
mesh_terms: D002099:Cacao / Q000235:genetics*; D003247:Conservation of Natural Resources; D004247:DNA / Q000302:isolation & purification; D019075:Electrophoresis, Capillary; D014644:Genetic Variation; D005838:Genotype; D005843:Geography; D010568:Peru; D018515:Plant Leaves / Q000235:genetics; D016133:Polymerase Chain Reaction
chemical_list: D004247:DNA