Morphological and genetic diversity of cacao (Theobroma cacao L.) in Uganda

  • David Gopaulchan
  • Lambert A. MotilalEmail author
  • Frances L. Bekele
  • Séverine Clause
  • James O. Ariko
  • Harriet P. Ejang
  • Pathmanathan Umaharan
Research Article


Cocoa is among the top foreign exchange earners in Uganda’s agriculture sector and has benefitted the livelihood of farmers involved in production. Although cacao cultivation was adopted in the early 1900s, little is known about the on-farm diversity of the crop. A total of 125 cacao landraces were surveyed from eight districts in the Central and Western Regions to evaluate the morphological and genetic diversity of cacao in Uganda. Passport data included site, tree, fruit and seed information. Trees were genotyped using 96 single nucleotide polymorphism markers on a Fluidigm platform. Low heterozygosity was detected in the germplasm in both the Central [observed heterozygosity (Ho) = 0.295, expected heterozygosity (He) = 0.334] and Western Regions (Ho = 0.317, He = 0.322). Genetic variation in both regions was generally comparable but the regions could be differentiated from each other. Inbreeding was noted in the Central Region while a greater sharing of genetic material was observed in the Western Region. The morphological and genetic data indicated that the Ugandan collection was an interspersed group with low to moderate variation with some separation of the Central from Western regions. Ancestry analysis indicated that the majority of the accessions were hybrids of Marañon lineage but also had Amelonado and Iquitos genetic backgrounds. These findings are consistent with the history of the movement of cacao into Uganda. A core collection of 18 individuals to represent the genetic diversity as well as 12 additional trees with possible advantageous traits is proposed.


Africa DNA fingerprinting Single nucleotide polymorphism Cacao landraces Passport data Population structure 



The authors are grateful to Saila Ramkissoon and Amrita Mahabir for their assistance in extracting DNA from the collected cacao leaf samples. SNP genotyping was supported by the International Fine Cocoa Innovation Centre (IFCIC), of the Cocoa Research Centre, which is funded by the European Union under the ACP Science & Technology Programme II and The University of the West Indies.

Compliance with ethical standards

Conflict of interest

The authors declare they have no conflict of interest.

Supplementary material

12298_2018_632_MOESM1_ESM.xlsx (17 kb)
Supplementary material 1 (XLSX 16 kb)


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Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2019

Authors and Affiliations

  1. 1.Cocoa Research CentreThe University of the West IndiesSt. AugustineRepublic of Trinidad and Tobago
  2. 2.Sunshine Agro Products LtdBrusselsBelgium

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