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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #190099

Title: Microsatellite Markers developed from Theobroma Cacao L. Expressed Sequence Tags

item Borrone, James
item Brown, James
item Schnell Ii, Raymond

Submitted to: Molecular Ecology Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2006
Publication Date: 7/1/2007
Citation: Borrone, J.W., Brown, J.S., Kuhn, D.N., Schnell II, R.J. 2007. Microsatellite Markers developed from Theobroma Cacao L. Expressed Sequence Tags. Molecular Ecology Notes.7:236-239.

Interpretive Summary: Using sequence information already available, 28 new informative genetic markers were developed for cacao (Theobroma cacao L.). These markers were used to identify accessions from one other, identify one off-type individual 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 molecular markers for Theobroma cacao.

Technical Abstract: Data-mining for expressed sequence tags (ESTs) containing simple sequence repeats (SSRs) has been demonstrated as an alternative method to generate genetic markers. The advantages are two-fold: the cost of identifying and developing useful markers is greatly reduced, and a putative function may be assigned to the locus based upon the sequence homology. We investigated converting ESTs isolated from Theobroma cacao L. into useful genetic markers for fingerprinting individuals and integration into genetic linkage maps. ESTs submitted into GenBank as of May 2005 were converted into a set of 2336 unigenes. Two hundred ten unigenes were identified as containing 293 SSRs, with AG-rich repeats dominating all size ranges. Primers were designed to 44 SSR-containing unigenes, 30 primer pairs gave polymerase chain reaction (PCR) products of the expected size. Twenty-six primer pairs were polymorphic and 28 potential loci could be mapped in at least one segregating population, with two primer pairs amplifying an additional product. Two primer pairs mapped three novel loci in an existing linkage map of an F2 population segregating for resistance to witches’ broom disease, and five primer pairs distinguished one off type individual among 65 trees representing 22 cultivars. The overall 60% success rate suggests that approximately 120 useful SSR-EST markers can be developed from the current T. cacao unigene set for genetic mapping and fingerprinting.