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United States Department of Agriculture

Agricultural Research Service


Location: Subtropical Horticulture Research

Title: A genetically anchored physical map of the cacao genome

item Blackmon, Barbara
item Saski, Christopher
item Schnell Ii, Raymond
item Motamayor, Juan
item Kuhn, David

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/11/2010
Publication Date: 1/11/2010
Citation: Blackmon, B., Saski, C., Schnell Ii, R.J., Motamayor, J.C., Kuhn, D.N. 2010. A genetically anchored physical map of the cacao genome. Plant and Animal Genome Conference. 1.

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. Currently there are about 500 molecular genetic markers for cacao and we are taking advantage of the cacao genome sequencing project to expand that to greater than 50,000 single-nucleotide polymorphism (SNP) markers. We will use these markers to improve the resolution of our current genetic maps and to find associations between specific SNPs and advantageous traits such as disease resistance or higher yield. The physical map is a critical step in the assembly of the genome sequence and the resulting identification of markers for the mapped traits. 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: Mars Incorporated and the United States Department of Agriculture have undertaken the sequencing of the genome of Theobroma cacao, which produces cocoa beans, the key ingredient in chocolate. Genetic information, such as whole genome sequence is necessary to better understand and improve cacao. In most genomic projects, a physical map is considered the centerpiece of genome research. A comprehensive integrated genetic and physical framework is invaluable for aligning the resulting sequence contigs, which are positioned onto the map by comparison to BAC-end sequence, electronic fingerprints and other lab-based methods. The Clemson University Genomics Institute (CUGI) has developed a genetically anchored physical map of cacao genome. Three BAC libraries were fingerprinted by high information content fingerprinting (HICF) representing the cacao genome approximately 30 times. 250 genetic markers from the genetic recombination map have been integrated with the physical map by pooled overgo hybridization. Based on a 440Mbp genome, our fingerprinting resulted in 295 contigs ranging from 50kb to greater than 10 Mbp in size. According to the consensus band (CB) units, we estimate to have anchored 72% and captured up to 96% of the cacao genome. The development of a genetically anchored physical map for cacao will be discussed.

Last Modified: 10/16/2017
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