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Genetic Diversity and Natural Population Structure of Cacao (Theobroma cacao L.) from the Brazilian Amazon Evaluated by Microsatellite Markers

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Abstract

A sample of 94 accessions of Theobroma cacao L. (cacao), representing four populations from the Brazilian Amazon (Acre, Rondônia, lower Amazon and upper Amazon) were analyzed using microsatellite markers to assess the genetic diversity and the natural population structure. From the 19 microsatellite loci tested, 11 amplified scorable products, revealing a total of 49 alleles, including two monomorphic loci. The Brazilian upper Amazon population contained the largest genetic diversity, with the most polymorphic loci, the highest observed heterozygosity; and the majority of rare alleles, thereby this region might be considered part of the center of diversity of the species. The observed heterozygosity for all the Brazilian populations (Ho = 0.347) was comparable with values reported for other similar upper Amazon Forastero cacao populations, with the Acre and Rondônia displaying the lowest values. The lower Amazon population, traditionally defined as highly homozygous, presented an unexpectedly high observed heterozygosity (Ho = 0.372), disclosing rare and distinct alleles, with large identity with the upper Amazon population. It was hypothesized that part of the lower Amazon population might derive from successive natural or intentional introduction of planting material from other provenances, mainly upper Amazon. Most of the loci exhibited a lower observed heterozygosity than expected, suggesting that self-pollination might be more common than usually assumed in cacao, but excess of homozygotes might also derive from sub-grouping (Wahlund effect) or from sampling related individuals. Most of the gene diversity was found to occur within groups, with small differentiation between the four Brazilian Amazon populations, typical of species with high gene flow.

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Abbreviations

AFLP:

amplified fragment length polymorphism

bp:

base pairs

CAB:

Cacao Amazon Brazil

cDNA:

complementary DNA

CIRAD:

“Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement”

CTAB:

hexadecytrimethyl ammonium bromide

dNTPs:

deoxyribonucleotides

EDTA:

ethylenediaminetetraacetic acid

ERJOH:

“Estação de Recursos Genéticos do Cacau José Haroldo”

RAPD:

random amplified polymorphic DNA

rDNA:

ribosomal DNA

RFLP:

restriction fragment length polymorphism

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Authors and Affiliations

  1. Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Av. Pádua Dias, 11, CP 83, Piracicaba, SP, 13400-970, Brazil

    Maria L. Sereno, Roland Vencovsky & Antonio Figueira

  2. ERJOH, Comissão Executiva do Plano da Lavoura Cacaueira, BR 316 km 17, CP 46, Marituba, 67105-970, PA, Brazil

    Paulo S. B. Albuquerque

Authors
  1. Maria L. Sereno
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  2. Paulo S. B. Albuquerque
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  3. Roland Vencovsky
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  4. Antonio Figueira
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Correspondence to Antonio Figueira.

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Sereno, M.L., Albuquerque, P.S.B., Vencovsky, R. et al. Genetic Diversity and Natural Population Structure of Cacao (Theobroma cacao L.) from the Brazilian Amazon Evaluated by Microsatellite Markers. Conserv Genet 7, 13–24 (2006). https://doi.org/10.1007/s10592-005-7568-0

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