Figure 2

Retrotransposon-based molecular marker methods. (a–c) Alternative priming sites in the genome paired with a priming site in a retrotransposon. (a) The SSAP method. Amplification is carried out from genomic DNA cut with two restriction enzymes (R1 and R2), containing a retrotransposon and ligated to an adapter (shown only for R2). Primers are indicated as arrows; the LTR generally serves as the retrotransposon priming site. (b) The IRAP method. The second priming site is also a retrotransposon. (c) The REMAP method. Amplification takes place between a microsatellite domain (labeled simple sequence repeat (SSR)) and a retrotransposon, using a primer anchored to the proximal side of the microsatellite and a retrotransposon primer. (d, e) RBIP. (d) Full sites are scored by amplification between a primer in the flanking genomic DNA (shown as a blue wavy line) and a retrotransposon primer. The single product is shown as a red bar beneath the diagram. The alternative reaction between the primers for the left and right flanks (light blue bar beneath the diagram) is inhibited in the occupied site by the length of the retrotransposon. (e) The flanking RBIP primers are able to amplify the empty site, depicted as a deep blue bar beneath the diagram, but amplification from the retrotransposon primer does not occur (missing product shown as a light red bar) because the TE insert is missing.