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The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao

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Evidence for the impact of mislabeling and/or pollen contamination on consistency of field performance has been lacking to reinforce the need for strict adherence to quality control protocols in cacao seed garden and germplasm plot management. The present study used SNP fingerprinting at 64 loci to examine the diversity, labeling errors and parentage in 2551 trees obtained from six seed gardens, breeders clone collection and single-cross progenies and a sample of farmers’ trees in Ghana. Clone mislabeling was pervasive, both within the seed garden clones and among clones of the breeders’ active collection. Among the seed garden clones, mislabeled trees were assigned to other parental clones used in the seed garden, pointing to labeling errors prior to planting as the principal cause of mislabeling. Among the breeders’ clone collection, both homonymous and synonymous mislabeling were identified in addition to trees with unique genotypes. This implicates pre-planting labeling errors and rootstocks overtaking budded scions. Parentage analysis supported the Amelonado ancestry of farmers’ varieties but with significant contribution of Upper Amazon introductions. Parentage of recently developed clones and of progenies of controlled crosses showed evidence of both pollen contamination and effects of mislabeled parents. The observed patterns of unexpected parentage had direct effects on the consistency of the variety performance between trials and increased within-plot variability for families with mixed ancestry. The results provide a strong basis for mainstreaming SNP fingerprinting in cacao breeding programs to improve the efficiency of the variety development process.

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This research was financed in part by a grant from Mars Incorporated through the African Cacao Initiative of the World Cacao Foundation (WCF/ACI) and the Ghana Cacao Board. The paper is published with permission of the Executive Director of the Cacao Research Institute of Ghana as manuscript number CRIG/03/2015/028/001.

Ethical standards

The research conducted was in compliance with the laws of the country in which the research was conducted.

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The authors declare that they have no conflict of interest.

Data archiving statement

SNP markers used for the parentage analyses are supplied as Supplementary Table S1. The list of the germplasm used and their levels of henerozygosity based on the SNP markers are indicated in the Supplementary Table S3. Raw SNP genotype data will be uploaded to the International Cacao Germplasm Database (; Turnbull and Hadley 2013)

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Correspondence to Francis K. Padi.

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Communicated by D. Grattapaglia

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Padi, F.K., Ofori, A., Takrama, J. et al. The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao. Tree Genetics & Genomes 11, 44 (2015).

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