Abstract
Accurate identification of individual genotypes is important for cacao ( Theobroma cacao L.) breeding, germplasm conservation and seed propagation. The development of single nucleotide polymorphism (SNP) markers in cacao offers an effective way to use a high-throughput genotyping system for cacao genotype verification. In the present study, high-throughput genotyping with SNP markers was used to fingerprint 160 cacao trees in the germplasm collection at the Cocoa Research Institute of Ghana (CRIG). These accessions had been originally introduced from international germplasm collections. The multilocus SNP profiles, generated by the Sequenom Mass Spectrometry platform, were compared with the SNP profiles of reference trees maintained in the international cacao collections. The comparison unambiguously identified mislabeled trees. For materials introduced as hybrid seeds without an available reference genotype, parentage analysis and model-based assignment were applied to verify their recorded parentage and genetic background. Our study shows that a small set of polymorphic SNP markers can provide a robust and accurate result for cacao genotype identification. This protocol can be applied for large-scale genotyping of cacao as well as for many other crops. Keywords: Cacao, conservation, chocolate, DNA fingerprint, molecular marker, tropical plant, off-type, true-to-type, West Africa. African Journal of Biotechnology , Vol 13(21), 2127-2136
Highlights
Cacao (Theobroma cacao L.) is an important tropical tree crop that provides raw ingredients for the chocolate confectionery industries
Based on the level of polymorphism and on their distribution across the ten chromosomes in cacao, 54 Single nucleotide polymorphism (SNP) markers were selected from 1560 candidate SNPs that had been developed using cDNA sequences from a wide range of cacao tissues (Argout et al, 2008)
The heterozygosity and polymorphic information index (PIC) of these SNP markers has been reported by Ji et al (2013)
Summary
Cacao (Theobroma cacao L.) is an important tropical tree crop that provides raw ingredients for the chocolate confectionery industries. Of which 75% was produced in West Africa. Ghana alone produced 850,000 tons of cacao, accounting for 21% of the world’s total output in 2010 (FAOSTAT, http://faostat3.fao.org/home/index.html). Cacao originated in the Amazon rainforest in South America and was domesticated by the Maya and Olmec peoples at least
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