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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement of Cacao Through Genomics-Assisted Breeding

Location: Subtropical Horticulture Research

Title: Genome Size Evolution in Theobroma cacao: Recent Sequencing of Two Cacao Genomes of Different Size

item Kuhn, David
item Ma, Jianxin
item Zheng, Ping
item Main, Dorrie
item Haiminen, Niina
item Parida, Laxmi
item Cornejo, Omar
item Findley, Seth
item Livingstone Iii, Donald
item Mustiga, Guiliana
item Schnell, Raymond
item Mockaitis, Keithanne
item Motamayor, Juan Carlos

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2013
Publication Date: 1/13/2013
Citation: Kuhn, D.N., Ma, J., Zheng, P., Main, D., Haiminen, N., Parida, L., Cornejo, O., Findley, S., Livingstone Iii, D.S., Mustiga, G., Schnell, R.J., Mockaitis, K., Motamayor, J. 2013. Genome Size Evolution in Theobroma cacao: Recent Sequencing of Two Cacao Genomes of Different Size. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.

Interpretive Summary:

Technical Abstract: 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. Cacao (Theobroma cacao L.) is a tropical understory tree whose seeds are the source of cocoa butter and cocoa for chocolate production. Two complete cacao genome de novo assemblies have been accomplished from two cacao cultivars ('Matina 1-6' and 'Criollo B1-97/B2') with genomes differing in size by approximately 9%. Different scales of amplification of transposable elements, particularly LTR-retrotransposons are largely responsible for the observed genome size difference. The genome size of genetic subpopulations of Theobroma cacao as well as individuals of other Theobroma species and a related genus, Herrania, have been estimated by flow cytometry and correlated to phylogeny and geographic origin. Probes made from centromeric repeats have been used with BAC probes to identify each of the 10 chromosomes of cacao and associate them with linkage groups from the genetic recombination map. The two cacao genomes will be compared in detail with regard to gene content, types, number and positions of transposable elements, and synteny. 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.

Last Modified: 10/20/2017
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