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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO Title: Design and implementation of the cacao genome database

item Zheng, Ping -
item Jung, Sook -
item Staton, Margaret -
item Svancera, Randall -
item Lee, Taein -
item Ficklin, Stephen -
item Kuhn, David
item Schnell Ii, Raymond
item Motamayor, Juan -
item Main, Dorrie -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 11, 2010
Publication Date: January 15, 2010
Citation: Zheng, P., Jung, S., Staton, M., Svancera, R., Lee, T., Ficklin, S., Kuhn, D.N., Schnell Ii, R.J., Motamayor, J.C., Main, D. 2010. Design and implementation of the cacao genome database. 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 web-based Cacao Genome Database will make our results available to cacao breeders and research scientists around the world. 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: The Cacao Genome Database (CGD, is being developed to provide a comprehensive data mining resource of genomic, genetic and breeding data for Theobroma cacao. Designed using Chado and a collection of Drupal modules, known as Tripal, CGD currently contains the genetically anchored cacao physical map, annotated transcript databases, maps and markers, all publicly available cacao sequences and the raw and assembled output of the ongoing genome sequencing project. Annotations of transcripts and genomic sequence include contig assembly, putative function and ontologies, simple sequence repeats, ORFs, and anchored position to the cacao physical map where applicable. Further Drupal modules are being developed to provide access to data and tools for molecular biologists, molecular geneticists and breeders.

Last Modified: 11/29/2015
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