CLASSIFYING JAPONICA RICE CULTIVARS WITH RAPD MARKERS

Two major subspecies of rice (Oryza sativa L.), indica and japonica, a re widely recognized. Japonica rice, which includes temperate and upla nd (tropical) cultivars, has been less well characterized by DNA marke rs than indica rice. The present study was undertaken to quantify gene tic diversity with random amplified polymorphic DNA (RAPD) markers in a sample of 134 predominately japonica cultivars and two wild species (O. nivara Sharma et Shastry and O. rufipogon Griffith). Ten oligonucl eotide primers produced 30 bands showing clear polymorphisms. The indi ca and japonica cultivars were classified into separate groups by clus ter analysis. Clustering was less pronounced within the japonica group . Tropical japonicas (including U.S. long-grain types) usually cluster ed together but no firm boundary was found between the tropical and te mperate types. Canonical discriminant analysis indicated that the dist ance between the indica group and each japonica subgroup was approxima tely equal and was much greater than the distance between the two japo nica subgroups. Additional primers led to better resolution of closely related cultivars. Genetic distances estimated from RAPD banding patt erns were correlated with those estimated by coefficients of parentage (r = 0.59, P < 0.001). In conclusion, RAPDs are useful for classifica tion of japonica rice cultivars, but many primers will be needed to re solve closely related japonica cultivars. Maximum genetic diversity fo r gene mapping or exploiting F-1 hybrid vigor within japonica cultivar s can be obtained in crosses between selected temperate (or U.S. short and medium grain) and tropical (or U.S. long grain) parents.