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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO

Location: Subtropical Horticulture Research

Title: Evaluating Theobroma grandiflorum for comparative genomic studies with Theobroma cacao

Authors
item Kuhn, David
item Figueira, Antonio -
item Lopes, Uilson -
item Motamayor, Juan -
item Meerow, Alan
item Cariaga, Kathleen
item Freeman, Barbara
item Livingstone, Donald
item Schnell Ii, Raymond

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 16, 2010
Publication Date: June 3, 2010
Repository URL: http://DOI 10.1007/s11295-010-0291-0
Citation: Kuhn, D.N., Figueira, A., Lopes, U., Motamayor, J., Meerow, A.W., Cariaga, K.A., Freeman, B.L., Livingstone, D., Schnell Ii, R.J. 2010. Evaluating Theobroma grandiflorum for comparative genomic studies with Theobroma cacao. Tree Genetics and Genomes. DOI 10.1007/s11295-010-0291-0

Interpretive Summary: The seeds of Theobroma cacao (cacao) are the source of cocoa, the raw material for the multi-billion dollar chocolate industry. Cacao’s two most important traits are its unique seed storage triglyceride (cocoa butter) and the flavor of its fermented beans (chocolate) and we would like to find the genes that regulate these traits. Since all cacao trees have seeds that, when fermented, taste like chocolate, we are looking at other trees in the genus Theobroma to compare to cacao. The USDA, IBM and Mars, Inc. are collaborating to sequence the cacao genome. In this paper, we evaluate Theobroma grandiflorum as a possible candidate for a comparative genomic study by looking at the performance in T. grandiflorum of three different types of molecular genetic marker originally developed in T. cacao. In addition, we use two specific markers to identify inter-specific hybrids between T. cacao and T. grandiflorum. Sequence conservation was significant and species-specific differences numerous enough to suggest that comparative genomics of T. grandiflorum and T. cacao will be useful in elucidating the genetic differences that lead to a variety of important agronomic trait differences. These findings will be of interest to scientists and cacao breeders working on the improvement of agronomic traits in cacao.

Technical Abstract: The seeds of Theobroma cacao (cacao) are the source of cocoa, the raw material for the multi-billion dollar chocolate industry. Cacao’s two most important traits are its unique seed storage triglyceride (cocoa butter) and the flavor of its fermented beans (chocolate). The genome of T. cacao is being sequenced, and to expand the utility of the genome sequence to the improvement of cacao, we are evaluating Theobroma grandiflorum, a closely related species, for its potential use in a comparative genomic study. T. grandiflorum differs from cacao in important agronomic traits such as flavor of the fermented beans, disease resistance to witches’ broom and abscission of mature fruits. By comparing genomic sequences and analyzing viable inter-specific hybrids, we hope to identify the key genes that regulate cacao’s most important traits. We have investigated the utility in T. grandiflorum of three types of markers (microsatellite markers, single-strand conformational polymorphism (SSCP) markers and single nucleotide polymorphism (SNP) markers) developed in cacao. Through sequencing of amplicons of twelve diverse individuals of both cacao and T. grandiflorum, we have identified new intra- and inter-specific SNPs. Two markers which had no overlap of alleles between the species were used to genotype putative inter-specific hybrid seedlings. Sequence conservation was significant and species-specific differences numerous enough to suggest that comparative genomics of T. grandiflorum and T. cacao will be useful in elucidating the genetic differences that lead to a variety of important agronomic trait differences.

Last Modified: 4/24/2014