MITE-transposon display efficiently detects polymorphisms among the Oryza AA-genome species

Abstract

Miniature inverted repeat transposable elements (MITEs) are a major component of interspersed repetitive sequences in the rice genome. These elements serve as excellent tools for fine genomic analysis throughout the genome. Using the rice genome database, we evaluated MITEs present in a 200-kb region surrounding the rice waxy locus and selected four MITE subfamilies for MITE-transposon display (MITE-TD) analyses. MITE-TD, which is an AFLP-related technique based on MITE sequences, was applied to detect polymorphisms among the AA-genome Oryza species using the four selected MITEs. The MITE-TD used here enabled the most efficient detection of polymorphisms of all the molecular marker techniques applied to date in the Oryza species. Of the four MITEs, Mashu, a new MITE family, was found to be the best system for detecting the polymorphisms, with a detection frequency 3-1.5 times higher than that of the other three MITEs. The MITE-TDs also revealed information about genetic variations within the AA-genome species, and the complexity of the genetic relationships between O. sativa and O. rufipogon.