Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Workshop: Aquaculture
            

ASSOCIATIONS BETWEEN MICROSATELLITES AND REPETITIVE ELEMENTS IN BIVALVE GENOMES

¹ College of Marine Studies, University of Delaware, 700 Pilottown Road, Lewes, DE, 19958, USA

A typically high degree of polymorphism and genomic abundance has made microsatellites increasingly popular as markers for use in linkage mapping and population genetics. PCR primers are targeted to presumably unique sequences flanking the simple sequence repeat region, yielding discrete single-locus polymorphisms. However, if the sequences flanking the microsatellite are not unique, amplification artifacts may occur, reducing the proportion of tested primer sets that yield useful markers. Analysis of microsatellite sequences present in a 0.7 Mb genomic sequence database from the eastern oyster Crassostrea virginica shows that many microsatellites, particularly those with tri- and tetranucleotide motifs, are embedded in or associated with repetitive flanking sequences. Searches of available sequence data from other bivalve species demonstrate similar patterns. Characterization of microsatellite-associated repetitive sequences will allow informed selection of microsatellite motifs during the enrichment and screening stages of marker development, as well as more efficient primer design. Application of this approach to marker development in C. virginica is discussed.