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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: Sequencing the Cacao Genome: Overall Strategy and SNP Discovery for Cacao Improvement.

Authors
item Kuhn, David
item Schnell Ii, Raymond
item Livingstone, Donald
item Scheffler, Brian - USDA-ARS MSA GENOMICS LAB
item Motamayor, Juan-Carlos - MARS, INC.
item Shapiro, Howard-Yana - MARS, INC.
item Bennett, Alan - UC DAVIS, DEPT OF VEGI CR
item Main, Dorrie - WSU, DEP OF HORT&LNDSC AR
item Blackmon, Barbara - CUGI, CLEMSON SC
item Saski, Chris - CUGI, CLEMSON SC
item Dean, Mark - IBM, WATSON RES CENTER
item Rigoutsos, Isidore - IBM, WATSON RES CENTER

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 12, 2009
Publication Date: January 12, 2009
Citation: Kuhn, D.N., Schnell Ii, R.J., Livingstone, D., Scheffler, B., Motamayor, J., Shapiro, H., Bennett, A., Main, D., Blackmon, B., Saski, C., Dean, M., Rigoutsos, I. 2009. Sequencing the Cacao Genome: Overall Strategy and SNP Discovery for Cacao Improvement.. Plant and Animal Genome Conference.

Interpretive Summary: The United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Mars, Incorporated, and IBM are combining their scientific resources to sequence and analyze the entire cocoa genome. Sequencing the cocoa genome is a significant scientific step that may allow more directed breeding of cocoa plants and perhaps even enhance the quality of cocoa, the key ingredient in chocolate. The collaboration may enable farmers to plant better quality cocoa and, more importantly, help create healthier, stronger cocoa crops with higher yields, pest and disease resistance, and increased water and nutrient use efficiency. These crops may help protect an important social, economic and environmental driver in Africa, where 70 percent of the world’s cocoa is produced. Additionally, the research results will be freely available to anyone through the Public Intellectual Property Resource for Agriculture (PIPRA), which supports agricultural innovation for both humanitarian and small-scale commercial purposes. Genome sequencing may help eliminate much of the guess-work of traditional breeding. If the sequencing is completed, it is hoped that scientists and farmers will be able to better identify the specific genetic traits that allow cocoa plants to produce higher yields and resist drought or pests. Then, cocoa breeders may be able to grow plants with these desirable traits to produce unique, new lines of cocoa plants using conventional breeding techniques.

Technical Abstract: On June 26, 2008, the United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Mars, Incorporated, and IBM announced that they are combining their scientific resources to sequence and analyze the entire genome of Theobroma cacao L., an understory tree from the Amazon basin whose beans are the basic component of cocoa and chocolate. Cacao is an out-crossing diploid (n=x=10) with a relatively small genome of ~440 Mb. Sequencing the cacao genome will accelerate marker-assisted selection (MAS) of cacao and has the potential to provide positive social, economic and environmental impact for more than 6.5 million small family cacao farmers around the world. Clemson University Genomics Institute (CUGI) is currently producing BAC libraries and a physical map and positioning ~350 mapped microsatellite markers. USDA-ARS will perform whole genome shotgun sequencing of a highly homozygous cultivar to generate a backbone. SNP discovery using next-generation sequencing of both cDNA and genomic DNA of genetically diverse cultivars will help saturate the cacao genetic map and make possible further association studies with the cacao germplasm collection. Researchers at the IBM Watson Research Center will use their computational biology expertise to assemble and study the cacao genome. Washington State University will facilitate the annotation and curation of the genome sequence in a publicly available database under the auspices of Public Intellectual Property Resource for Agriculture (PIPRA) to guarantee free access to the data in real time. Mars, Incorporated, the world’s largest chocolate company, is financially backing and coordinating this project.

Last Modified: 10/31/2014
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