In plants, phenotypic variations have generally been found to be caused by genetic changes. However, it has recently been shown that phenotypic variations can also be potentially caused by epigenetic changes due to aberrant methylation states. To survey polymorphisms in methylation states in the genomic segments from nine strains of Oryza sativa and O. rufipogon, we employed the methylation-sensitive amplified polymorphism (MSAP) method based on AFLP analysis using isoschizomers differing in

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... ir methylation sensitivity, HpaII and MspI. In addition to MSAP analysis, we applied the MITE-transposon-display method to detect methylation-sensitive MITE-flanking polymorphisms (MSMPs) for surveying the methylation state of the genomes. The frequency of occurrence of the methylated fragments detected by these analyses varied depending on the three primers targeting two different MITE sequences for MSMP and EcoRI sites for MSAP. This suggests that MITEs are associated with the methylation state in their proximal regions. Comparison of the fragment patterns between any two of the nine strains revealed polymorphisms of the methylation state referred to as epigenetic markers (epi-markers). A phylogenetic tree based on epi-markers within nonpolymorphic fragments was analogous to that based on genetic markers. On the other hand, the proportion of epi-markers in the total number of fragments was constant at 2-3% in all the combinations of two strains. Our results enabled us to predict that the epi-markers are potentially linked to phenotypic variations, and that this possibility is more likely to occur between closely related strains.