IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques

The BARE-1 retrotransposon is an active. dispersed, and highly abundant com ponent of the genome of barley (Hordeum vulgare) and other species in its g enus. Like all retrotransposons of its kind, BARE-1 is bounded by long term inal repeats (LTRs). We have developed two amplification-based marker metho ds based on the position of given LTRs within the genome. The IRAP (Inter-R etrotransposon Amplified Polymorphism) markers are generated by the proximi ty of two LTRs using outward-facing primers annealing to LTR target sequenc es. In REMAP (REtrotransposon-Microsatellite Amplified Polymorphism), ampli fication between LTRs proximal to simple sequence repeats such as constitut e microsatellites produces markers. The methods can distinguish between bar ley varieties and produce fingerprint patterns for species across the genus . The patterns indicate that although the BARE-1 family of retrotransposons is disperse, these elements are locally clustered or nested and often foun d near tandem arrays of a simple sequence repeat.