Tree Genetics & Genomes

, 14:32 | Cite as

Genetic identity and diversity of Nigerian cacao genebank collections verified by single nucleotide polymorphisms (SNPs): a guide to field genebank management and utilization

  • Festus O. Olasupo
  • Daniel B. Adewale
  • Peter O. Aikpokpodion
  • Anna A. Muyiwa
  • Ranjana Bhattacharjee
  • Osman A. Gutierrez
  • Juan Carlos Motamayor
  • Raymond J. Schnell
  • Sona Ebai
  • Dapeng Zhang
Original Article
Part of the following topical collections:
  1. Germplasm Diversity


Nigeria is the sixth largest cacao producer in the world. Field performance and quality of cacao hybrid families is largely dependent on the genetic integrity of parental clones obtained in field genebank collections. However, information on the impact of mislabeling on seed garden output in Nigeria is lacking. Using 63 single nucleotide polymorphism (SNP) markers, we analyzed 1457 cacao trees sampled from seven major field genebank plots in Nigeria to assess the genetic integrity in Nigerian cacao germplasm. The procedure of multilocus matching with known reference clones revealed up to 78% mislabeling in recently introduced international germplasm. A high rate of mislabeling was also revealed in the West African local selections and breeding lines, using Bayesian assignment test. The problem of mislabeling has been attributed to errors from the sources of introduction, pre-planting labeling errors, and rootstocks overtaking budded scions due to poor field management. The analysis of genetic diversity revealed a good representation of the available cacao germplasm groups in Nigerian field genebanks, indicating that the genetic base of Nigeria cacao germplasm has been significantly widened through germplasm introductions. However, only a small proportion of the available germplasm in the genebank have been utilized for variety development. This study proved the utility of SNP markers for cleaning up the genebanks and reducing offtypes; thereby providing a strong basis for improving the accuracy and efficiency in cacao genebank management and breeding, as well as for mobilizing improved varieties to cacao farmers in Nigeria.


Chocolate tree Genetic integrity Mislabeling Off-types Tropical agriculture West Africa 



The authors express appreciation to the Executive Director of the Cocoa Research Institute of Nigeria for the permission granted to publish this paper. The invaluable support of field and laboratory staff during the execution of this work is gratefully acknowledged. The authors also thank Drs. Sue Mischke and Lyndel Meinhardt, USDA-ARS, for reviewing and editing this manuscript.

Data archiving statement

All row data for the Nigerian germplasm and the reference trees are being submitted to the International Cacao germplasm Database ( The full list of SNP markers and reference cacao accessions are included as Supplementary Materials of this manuscript.


The authors wish to acknowledge the World Cocoa Foundation’s African Cocoa Initiative for funding this study.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

11295_2018_1244_MOESM1_ESM.docx (57 kb)
ESM 1 (DOCX 57 kb)


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Copyright information

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

Authors and Affiliations

  • Festus O. Olasupo
    • 1
  • Daniel B. Adewale
    • 2
  • Peter O. Aikpokpodion
    • 3
  • Anna A. Muyiwa
    • 1
  • Ranjana Bhattacharjee
    • 4
  • Osman A. Gutierrez
    • 5
  • Juan Carlos Motamayor
    • 6
  • Raymond J. Schnell
    • 6
  • Sona Ebai
    • 7
  • Dapeng Zhang
    • 8
  1. 1.Crop Improvement DivisionCocoa Research Institute of NigeriaIbadanNigeria
  2. 2.Department of Crop Science and HorticultureFederal UniversityOyeNigeria
  3. 3.Department of Genetics and BiotechnologyUniversity of CalabarCalabarNigeria
  4. 4.Bioscience CenterInternational Institute of Tropical AgricultureIbadanNigeria
  5. 5.USDA-ARS Subtropical Horticulture Research StationMiamiUSA
  6. 6.Mars IncorporatedMiamiUSA
  7. 7.World Cocoa FoundationAccraGhana
  8. 8.USDA-ARS, NEA, BARC, SPCLBeltsvilleUSA

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