Cloning and mapping of telomere-associated sequences from rice

We have isolated three telomere-associated sequences from rice using cassette-ligation-mediated polymerase chain reaction (PCR). Each of the obtained clones hybridized to the terminal of one or several rice chromosome arms. The telomeres recognized by the clones displayed a high level of polymorphism between two rice varieties, Nipponbare (a japonica variety) and Kasalath (an indica variety). Variability in the chromosome termini was also detected among individual F2 progeny plants, which were derived from a cross between the two rice varieties. One clone containing telomere-associated sequences was located to one end of chromosome 5, and another clone to one end of chromosome 11. For another clone, non-allelic segregation of polymorphic hybridization bands was observed between japonica and indica rice; this clone was mapped to one end of chromosome 12 in japonica and to one end of chromosome 11 in indica rice. This indicates an exchange of termini between nonhomologous chromosomes.