Classifying Japonica Rice Cultivars with RAPD Markers

Abstract

Two major subspecies of rice (Oryza sativa L.), indica and japonica, are widely recognized. Japonica rice, which includes temperate and upland (tropical) cultivars, has been less well characterized by DNA markers than indica rice. The present study was undertaken to quantify genetic 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 oligonucleotide primers produced 30 bands showing clear polymorphisms. The indica and japonica cultivars were classified into separate groups by cluster analysis. Clustering was less pronounced within the japonica group. Tropical japonicas (including U.S. long‐grain types) usually clustered together but no firm boundary was found between the tropical and temperate types. Canonical discriminant analysis indicated that the distance between the indica group and each japonica subgroup was approximately equal and was much greater than the distance between the two japonica subgroups. Additional primers led to better resolution of closely related cultivars. Genetic distances estimated from RAPDb anding patterns were correlated with those estimated by coefficients of parentage (r = 0.59, P < 0.001). conclusion, RAPDasr e useful for classification of japonica rice cultivars, but many primers will be needed to resolve closely related japonica cuitivars. Maximumge netic diversity for gene mapping or exploiting F1 hybrid vigor within japonica cultivars can be obtained in crosses between selected temperate (or U.S. short and medium grain) and tropical (or U.S. long grain) parents.