Inter-MITE polymorphisms (IMP): a high throughput transposon-based genome mapping and fingerprinting approach

Miniature inverted-repeat transposable elements or MITEs represent a large superfamily of transposons that are moderately to highly repetitive and fre quently associated with plant genes. These attributes were exploited in the development of a powerful marker technology called Inter-MITE polymorphism , or IMP, which involves the amplification between two adjacent MITEs. In t his report, we describe the utility of the IMP approach in the mapping and fingerprinting of the barley genome. MITEs were systematically mined from b arley genomic gene sequences by computer-assisted database searches and str uctural analysis. Barley MITEs include members of the Stowaway family and a new family we have named Barfly. Using these barley MITEs, a total of 88 I MP markers were mapped onto an existing barley RFLP map that was based on a doubled-haploid segregating population between Hordeum vulgare and Hordeum spontaneum. We demonstrate that the IMP approach can be effectively applie d in the fingerprinting of barley cultivars and for genetic similarity anal ysis. We also provide evidence that barley MITE-based primers can be effect ively used in the mapping and fingerprinting of other cereals, suggesting t hat the IMP approach has broad applicability.