ARS | Publication request: Identification and mapping of conserved ortholog set(COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cocoa and comparative genomics studies

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 4, 2011
Publication Date: September 9, 2011
Repository URL: http://DOI 10.1007/s11295-011-0424-0
Citation: Kuhn, D.N., Livingstone, D., Main, D., Zheng, P., Saski, C., Feltus, F.A., Mockaitis, K., Farmer, A., May, G., Schnell Ii, R.J., Motamayor, J.C. 2011. Identification and mapping of conserved ortholog set(COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cocoa and comparative genomics studies. Tree Genetics and Genomes. 8:97–11.

Interpretive Summary: Theobroma cacao, whose seeds are the source of cocoa, the raw material for the multi-billion dollar chocolate industry, is an important tropical agriculture commodity that is affected by a number of fungal pathogens, including frosty pod (Moniliophthora roreri H.C. Evans, Stalpers, Samson & Benny) and witches’ broom (Moniliophthora perniciosa (Aime and Phillips-Mora comb. nov.). We are trying to find molecular genetic markers that are linked to disease resistance in Theobroma cacao to aid in a marker assisted selection (MAS) breeding program to ensure a reliable supply of cocoa for the US confectionary industry. In this paper, we identify 83 single-nucleotide polymorphism (SNP) markers, 19 of which are correlated with disease resistance or agronomic quantitative trait loci (QTL). 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 cultivars produced through our MAS breeding program.

Technical Abstract: Theobroma cacao is a tree cultivated in the tropics around the world for its seeds that are the source of both chocolate and cocoa butter. The cacao genome sequencing project initiated as a collaboration between USDA, Mars, Inc. and IBM has generated a great deal of transcriptome and genome sequence information, which we are rapidly employing in marker assisted selection programs in cocoa producing countries. Conserved ortholog set (COS)II genes are single-copy and have proved useful in syntenic studies to orient the genomes of different species. We have used three different strategies and three different types of cacao genetic and sequence data to identify and map 96 cacao COSII genes. With information from the SNP discovery project associated with the genome sequencing project, we have identified SNP markers for 83 mapped COSII genes for use in genotyping and off-typing in cacao breeding programs in cocoa-producing countries.