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United States Department of Agriculture

Agricultural Research Service

Title: Microsatellite-containing expressed sequence tags for genetic mapping and genotyping Theobroma cacao

Authors
item Borrone, James
item Schnell Ii, Raymond
item Brown, James
item Kuhn, David

Submitted to: Proceedings of the XVth International Cacao Conference
Publication Type: Proceedings
Publication Acceptance Date: June 30, 2006
Publication Date: October 1, 2007
Citation: Borrone, J.W., Schnell Ii, R.J., Brown, J.S., Kuhn, D.N. 2007. Microsatellite-containing expressed sequence tags for genetic mapping and genotyping Theobroma cacao. Proceedings of the XVth International Cacao Conference.

Interpretive Summary: Using sequence information already available we identified 210 unigenes containing microsatellites. We developed twenty-eight new informative genetic markers for cacao (Theobroma cacao L.) from a subset of these 210. These markers were used to identify accessions from one other, identify one off-type individual form from four other genetically related individuals, and were assessed for mapping into several T. cacao populations. As these markers are developed from expressed sequences identifying with genes potentially involved in flower and fruit production as well as disease resistance, they should be powerful markers in characterizing germplasm and for breeding of T. cacao cultivars with improved disease resistance and pod production. This is the first paper describing the development of ESTs into useful markers for Theobroma cacao.

Technical Abstract: Two high-density genetic maps for Theobroma cacao currently exist. Of the approximate 500 markers mapped, 270 are microsatellite markers. Microsatellite markers are preferred molecular markers due to their codominant inheritance, abundance, transferability, locus specificity, reproducibility, PCR-based methodology allowing high-throughput analyses requiring very little DNA, and high degree of polymorphism. Only 122 markers are shared between the two linkages maps, thus additional SSR markers are desirable for fingerprinting, comparative mapping, and quantitative trait loci (QTL) identification and localization. Generating novel microsatellite markers directly from genomic DNA is costly and time-consuming and successfully isolating novel, informative markers diminishes as the number of microsatellites characterized from an organism increases. Data-mining microsatellites from expressed sequence tags (ESTs) has proven effective for generating useful genetic molecular markers in a number of plant species. Microsatellite-containing ESTs can be rapidly developed into novel molecular genetic markers useful for QTL localization, genetic mapping, fingerprinting accessions, and comparative mapping among related species. Advantages of EST-derived microsatellites are a reduction in the time and cost to identify and develop novel markers, assignment of a putative function to the locus based upon sequence homology, and an increased probability of identifying markers associated with useful traits. Several laboratories are currently developing ESTs from Theobroma cacao. We evaluated the potential of identifying microsatellite-containing ESTs and developing them into useful genetic markers.

Last Modified: 11/21/2014
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