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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: T. cacao Transcriptome Sequencing

Authors
item Mockaitis, Keithanne -
item Kuhn, David
item Main, Dorrie -
item Haiminen, Niina -
item May, Greg -
item Saski, Chris -
item Scheffler, Brian
item Schnell Ii, Raymond
item Harkins, Tim -
item Motamayor, Juan -
item Shapiro, Howard -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 3, 2010
Publication Date: January 15, 2010
Citation: Mockaitis, K., Kuhn, D.N., Main, D., Haiminen, N., May, G., Saski, C., Scheffler, B.E., Schnell Ii, R.J., Harkins, T., Motamayor, J.C., Shapiro, H. 2010. T. cacao Transcriptome Sequencing. 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 and specifically the sequencing of the cacao leaf transcriptome 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. 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: To compliment the T. cacao genome sequencing initiative and to build a reference set of expressed genes for functional studies, a broad and state-of-the-art approach to transcriptome sequencing is underway. Using newly optimized methods, transcriptome sequencing libraries were prepared from RNA of organ-specific collections of Matina1-6, the chosen cacao genome sequence reference. De novo assemblies were generated using a newly released version of the 454 Newbler Assembler for cDNA analysis. Analysis of 1.5 M reads from 454 GS-FLX Titanium sequencing of a Matina1-6 leaf transcriptome library produced an assembly of 22,172 isotigs, representing individual transcripts of the reference tree. Earlier 159,320 cloned EST sequences derived from a variety of genotypes and tissue collections were assembled into 45,056 putative unigenes using CAP3 (Huang and Madan, 1999). Deep surveys of RNA samples from Matina1-6 and more highly polymorphic accessions were generated from Illumina GAII sequencing reads mapped to the above assemblies. Findings from these projects, additional 454 and Illumina mRNA sequencing results, as well as protein-coding functional annotation, will be presented to overview current collaborative efforts engaged in cacao gene discovery.

Last Modified: 9/2/2014