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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO

Location: Subtropical Horticulture Research

Title: Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm

Authors
item Zhang, Dapeng
item Livingstone, Donald
item Irish, Brian
item Kuhn, David
item Schnell Ii, Raymond
item Meinhardt, Lyndel

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 16, 2011
Publication Date: January 16, 2011
Citation: Zhang, D., Livingstone, D., Irish, B.M., Kuhn, D.N., Schnell II, R.J., Meinhardt, L.W. 2011. Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm. Annual International Plant & Animal Genome Conference. 2011.

Interpretive Summary: Theobroma cacao, the source of cocoa beans for chocolate, is an important tropical agriculture commodity that is affected by a number of fungal pathogens and insect pests, as well as concerns about yield and quality. We are trying to find molecular genetic markers that are linked to disease resistance and other important economic traits to aid in a marker assisted selection (MAS) breeding program for cacao to ensure a reliable supply of cocoa for the US confectionary industry. Accurate identification of individual genotypes in an efficient manner is especially important for cacao (Theobroma cacao L.) germplasm conservation and breeding. The development of single nucleotide polymorphism (SNP) markers in cacao offers the opportunity to use a high throughput genotyping system for cacao germplasm characterization. In the present study, a set of one hundred EST-derived SNP markers were tested against 350 cacao germplasm accessions representing diverse genetic populations, using Sequenom Mass Spectrometry genotyping platform. The result suggests that high throughput genotyping using a small set of SNP markers is highly accurate and a cost-effective means for cacao germplasm characterization. Our results are important to scientists trying to understand the mechanism of disease resistance and, eventually, to cacao farmers who will benefit from superior disease resistant and more productive cultivars produced through our MAS breeding program.

Technical Abstract: Accurate identification of individual genotypes in an efficient manner is especially important for cacao (Theobroma cacao L.) germplasm conservation and breeding. The development of single nucleotide polymorphism (SNP) markers in cacao offers the opportunity to use a high throughput genotyping system for cacao germplasm characterization. In the present study, a set of one hundred EST-derived SNP markers were tested against 350 cacao germlasm accessions representing diverse genetic populations, using Sequenom Mass Spectrometry genotyping platform. The SNP genotyping result was compared with the multi-locus data generated with 15 SSR loci, in terms of probability of identity, genetic distance, F-statistics, individual assignment probability in model based clustering analysis, parentage analysis and sibship reconstruction. Our study shows that the 75 polymorphic SNP markers provide more robust results than the 15 SSR markers in diversity analysis. The result suggests that high throughput genotyping using a small set of SNP markers is highly accurate and a cost-effective means for cacao germplasm characterization. The development of a core set of SNP markers for cacao genotyping and its potential applications in cacao germplasm management are discussed.

Last Modified: 9/23/2014
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