Tree Genetics & Genomes

, 14:52 | Cite as

Assessment of genetic diversity and structure in cocoa trees (Theobroma cacao L.) in Côte d’Ivoire with reference to their susceptibility to Cocoa swollen shoot virus disease (CSSVD)

  • Boguinard S. H. B. Guiraud
  • Mathias G. Tahi
  • Olivier Fouet
  • Caudou I. Trebissou
  • Désiré Pokou
  • Ronan Rivallan
  • Xavier Argout
  • Kouamé K. Koffi
  • Boaké Koné
  • Bi I. A. Zoro
  • Claire Lanaud
Original Article
Part of the following topical collections:
  1. Population structure


Resistance to Cocoa Swollen Shoot Virus disease (CSSVD) is becoming an increasingly important criterion for selection of new cocoa cultivars in Côte-d’Ivoire, where the disease resurfaced since 2003. This virus can seriously affect the yield of trees with a loss of 25%, 1 year after infection, to around 100% 3 years after. In order to find tolerant plant material, 337 farm accessions have been collected on fields affected by CSSVD, according to the status of accessions potentially tolerant (APT) or susceptible (APS). Both phenotypic groups were genotyped using 30 microsatellite markers (SSR) in the presence of representative clones of the ten genetic groups of cocoa. This study revealed 214 alleles with the set of primer pairs used. The number of alleles per locus was between 3 and 16 with an average of 7.13 alleles per locus. The results showed a high contribution of genetic diversity within population (Hs = 0.51) to the total genetic diversity (Ht = 0.53) for the two studied groups. There was no significant difference between tolerant and susceptible groups (Fst = 0.05). These results suggest that APT could be a potential genetic reservoir for other traits of interest associated with virus resistance. The phylogenetic tree, as the STRUCTURE analysis of Ivorian cocoa population, showed a distribution of individuals following four groups marked by a high contribution of group 4 (Nanay, Maranon, Guiana) followed by group 2 (Criollo), and group 1 (Amelonado), and a lower contribution of group 3 (Iquitos, Purus, Nacional, Curaray, Contamana).


Diversity Microsatellites Theobroma cacao L. CSSVD Côte d’Ivoire 



Authors also thank the Nangui Abrogoua University of Abidjan (Côte d’Ivoire), the National Agricultural Research Centre in Côte d'Ivoire (CNRA), and the International Centre for Agricultural Research and Development of France (CIRAD) for provision of plant material and molecular genotyping platform availability.

Data archiving statement

The data has been submitted to public databases
  • List and characteristic of samples

  • Molecular SRR data

  • The main results of software’s (Darwin 6, Genetix 4.05; GeneAlex 6, Structure 2.4.3)

  • The new phylogenetic tree with the names of individuals (revealed by Darwin) and variable contribution (revealed by Structure)

Funding information

This work was funded by the AMRUGE-CI scholarship. Mars, Inc. also provided financial contribution to this work.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Boguinard S. H. B. Guiraud
    • 1
    • 2
    • 3
    • 4
  • Mathias G. Tahi
    • 2
  • Olivier Fouet
    • 3
    • 4
  • Caudou I. Trebissou
    • 2
  • Désiré Pokou
    • 2
  • Ronan Rivallan
    • 3
    • 4
  • Xavier Argout
    • 3
    • 4
  • Kouamé K. Koffi
    • 1
  • Boaké Koné
    • 2
  • Bi I. A. Zoro
    • 1
  • Claire Lanaud
    • 3
    • 4
  1. 1.UFR des Sciences de la Nature, Unité de Phytotechnie et Amélioration génétiqueUniversité Nangui Abrogoua d’Abidjan (UNA)AbidjanCôte d’Ivoire
  2. 2.Programme cacao, Opération Amélioration variétaleCentre National de Recherche Agronomique (CNRA)DivoCôte d’Ivoire
  3. 3.Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD),UMR AGAPMontpellierFrance
  4. 4.AGAPUniv Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance

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