Anchor polymerase chain reaction display: A high-throughput method to resolve, score, and isolate dimorphic genetic markers based on interspersed repetitive DNA elements

Genes which confer a disease when mutated, or for which population variabil ity contributes to a quantitative trait such as longevity or disease suscep tibility, can be localized in the genetic map by use of an appropriately de nse set of polymorphic DNA markers. Here we describe an anchor PCR method f or high-throughput genotyping, which can be used to amplify the DNA segment s flanking an interspersed repetitive sequence such as a transposon, and to limit the number of product bands per reaction to facilitate marker resolu tion. We used this method to amplify and display DNA fragments flanking the Tc1 transposable elements from different strains of the nematode Caenorhab ditis elegans, varying widely in insert number, and to analyze marker segre gation in recombinant inbred lines generated from an interstrain cross. Sin ce essentially all eukaryotic genomes contain abundant interspersed repeat families, many of which are dimorphic (for presence or absence of specific elements) among populations, this method can be used for rapid genotyping a nd fine-scale chromosomal mapping in many species, including those for whic h extensive mapping and sequencing data do not yet exist. (C) 2000 Academic Press.