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

Abstract 

Miniature inverted-repeat transposable elements or MITEs represent a large superfamily of transposons that are moderately to highly repetitive and frequently 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 this report, we describe the utility of the IMP approach in the mapping and fingerprinting of the barley genome. MITEs were systematically mined from barley genomic gene sequences by computer-assisted database searches and structural 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 IMP 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 applied in the fingerprinting of barley cultivars and for genetic similarity analysis. We also provide evidence that barley MITE-based primers can be effectively used in the mapping and fingerprinting of other cereals, suggesting that the IMP approach has broad applicability.