Conformation polymorphisms and targeted marker development.

Genetic markers were developed for three targeted bovine loci using both single-stranded and double-stranded DNA conformation polymorphisms. Eight of nine DNA fragments exhibited single-stranded conformation polymorphisms while only one of nine exhibited a double-strand conformation polymorphism. All but one of the polymorphic fragments exhibited two allelic forms, with the exception being a single-stranded conformation polymorphism with three alleles. Utility of conformation polymorphisms relative to microsatellite markers for linkage map development and quantitative trait loci (QTL) mapping was assessed by comparing frequency of heterozygote parents from reference and resource families. Heterozygosity was greater for microsatellite markers (P < 0.01) and reference family parents (P < 0.01), though the disparity between marker types tended to be less dramatic for the reference family parents (P < 0.09). These results suggest conformation polymorphisms will be a useful tool for targeted marker development in linkage map and comparative map development provided genetically diverse families are studied.