Short tandem repeat polymorphic markers for the rat genome from marker-selected libraries

In an effort to generate a genome-wide set of high-quality polymorphic mark ers for the rat, we used the marker-selection method, which has already bee n proven useful for the development of markers, especially for the human ge nome. Small-insert (300-900 bp) rat genomic libraries were constructed with an estimated complexity of three genome equivalents and enriched for shea tandem repeat sequences (STRs). The enriched libraries were found to contai n 45% (CA)(n) and 27% (GATA)(n), representing at least a 50-fold enrichment over unselected small insert genomic libraries. A subset of 2160 STR-conta ining clones, primarily of the (GATA), class of repeats, were sequenced. PC R primers flanking the repeats were synthesized from some of the sequences from the (CA), and (GATA), classes of STRs and tested for polymorphism in a panel of eight inbred rat strains. This strategy yielded 147 polymorphic m arkers, which mapped with high odds to all chromosomes by linkage in three F-2 populations. The integration of these STR markers with other rat geneti c markers and mapping reagents will facilitate the mapping of disease genes in the rat and the identification of loci associated with complex mammalia n phenotypes.