Abstract
Polymorphic markers between closely related varieties of rice are necessary for the practical application of. molecular markers, such as restriction fragment length polymorphism (RFLP) markers, to rice breeding. In this study, we employed a representational difference analysis (RDA) to develop RFLP markers between closely related japonica varieties, Koshihikari and Akihikari. Three rounds of subtractive hybridization were performed, resulting in the isolation of 13 independent clones which showed RFLP between Koshihikari and Akihikari. These probes were unique and useful for mapping. Segregation of these markers in an F2 population derived from the cross between 2 varieties fitted the Mendelian expected ratio well, indicating that these clones were derived from the nuclear genome. Linkage analysis showed that these markers were separated into 2 groups and 5 unlinked markers. This is the first time that RDA was applied
