High frequency of sequence polymorphism in rice MITEs and application to efficient development of PCR-based markers

Abstract

Miniature inverted-repeat transposable elements (MITEs) are abundant genomic components in many plants including rice. In this study, in order to determine whether rice MITEs are rich in sequence polymorphism and useful for developing PCR-based markers, we compared the genomic sequences of a japonica rice variety, Asominori, and an indica rice variety, IR24, in terms of MITE and MITE-less regions. Fifteen rice loci that had been previously reported to include MITEs (Gaijin, Castaway, Ditto, Wanderer, Explorer and Stowaway) were selected. Genomic sequences including MITEs at the loci were determined and compared between Asominori and IR24. Genomic sequences of Asominori and IR24 for the regions corresponding to seven RFLP markers (C81, R2303, S10019, S10602, S12564, G291 and G2155) were used to provide data for MITE-less regions. It was demonstrated that the degree of sequence polymorphism between the two varieties was much higher in the MITE regions than in the MITE-less regions. Sequence polymorphism was detected in fourteen MITE regions out of the fifteen regions tested. We also selected six rice sequences showing a high homology with a Wanderer family from a public database and surveyed sequence polymorphism between Asominori and IR24 for the regions. Some degree of polymorphism was observed in each of the six family members of Wanderer. As a result, twenty PCR-based markers in total were developed utilizing MITEs in rice and mapped on a linkage map, indicating that PCR-based markers for genetic studies and breeding programs could be developed efficiently by using MITEs.