Cacao Genome Database

Authors: ZHENG, PING - Washington State University; LEE, TAEIN - Washington State University; FICKLIN, STEPHEN - Washington State University; JUNG, SOOK - Washington State University; BODAH, ELIANE THAINES - Washington State University; Kuhn, David; LIVINGSTONE III, DONALD - Mars, Inc; MOCKAITIS, KEITHANNE - Indiana University; GILBERT, DON - Indiana University; SCHNELL, RAYMOND - Mars, Inc; MAIN, DORRIE - Washington State University; MOTAMAYOR, JUAN CARLOS - Mars, Inc

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/15/2012
Publication Date: N/A
Citation: N/A

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. The Cacao Genome Database provides a comprehensive data mining resource of genomic and genetic data for the Theobroma cacao cv. Matina 1-6. The database contains the annotated T. cacao cv. Matina1-6 genome, annotated transcript databases, genetic maps and markers, and all publicly available cacao sequences All raw and analyzed data sets of T. cacao cv. Matina 1-6 are available to browse, search and download. The CGD was implemented and designed using Chado and a collection of Drupal modules, known as Tripal. CGD has public and private portals, with all private data password protected. Available visualization and analysis tools include Search, GBrowse, GBrowse-syn, CMap, SSR server, NCBI and Batch BLAST servers. The website is available in English and Portuguese. A breeders toolbox is being developed to provide breeders with access to secure and personalized breeding management databases that directly connect to the public genomic and genetic data relevant for furthering genomics-assisted breeding of cacao. The release of the cacao genome sequence on the CGD will provide researchers with access to the latest genomic tools, enabling more efficient research and accelerating the breeding process, thereby expediting the release of superior cacao cultivars as well as contribute to our basic knowledge of tree biology. CGD can be accessed at http:// www.cacaogenomedb.org. 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 provides a comprehensive data mining resource of genomic and genetic data for the Theobroma cacao cv. Matina 1-6. The database contains the annotated T. cacao cv. Matina1-6 genome, annotated transcript databases, genetic maps and markers, and all publicly available cacao sequences All raw and analyzed data sets of T. cacao cv. Matina 1-6 are available to browse, search and download. The CGD was implemented and designed using Chado and a collection of Drupal modules, known as Tripal. CGD has public and private portals, with all private data password protected. Available visualization and analysis tools include Search, GBrowse, GBrowse-syn, CMap, SSR server, NCBI and Batch BLAST servers. The website is available in English and Portuguese. A breeders toolbox is being developed to provide breeders with access to secure and personalized breeding management databases that directly connect to the public genomic and genetic data relevant for furthering genomics-assisted breeding of cacao. The release of the cacao genome sequence on the CGD will provide researchers with access to the latest genomic tools, enabling more efficient research and accelerating the breeding process, thereby expediting the release of superior cacao cultivars as well as contribute to our basic knowledge of tree biology. CGD can be accessed at http:// www.cacaogenomedb.org.