Determination of RAPD markers in rice and their conversion into sequence tagged sites (STSs) and STS-specific primers

We produced 102 randomly amplified polymorphic DNA (RAPD) markers mapped on all 12 chromosomes of rice using DNAs of cultivars Nipponbare (japonica) and Kasalath (indica) and of F2 population generated by a single cross of these parents. Sixty random primers 10 nucleotides long were used both singly and in random pairs and about 1,400 primer-pairs were tested. Using both agarose gel and polyacrylamide gel electrophoresis enabled us to detect polymorphisms appearing in the range from < 100 bp to 2 kb. The loci of the RAPD markers were determined onto the framework of our RFLP linkage map and some of these markers were mapped to regions with few markers. Out of the 102 RAPD markers, 20 STSs (sequence-tagged sites) and STS-specific primer pairs were determined by cloning, identifying and sequencing of the mapped polymorphic fragments.