Nuclear genome differentiation in Asian cultivated rice as revealed by RFLP analysis

RFLP analysis was carried out to clarify the nuclear genome differentiation in Asian rice varieties of Oryza sativa. Based on the restriction fragment patterns with two endonucleases, EcoRI and HindIII, using 12 single-copy rice DNA probes, 93 types of nuclear genome were found among 112 local varieties from 17 Asian countries. In a dendrogram showing genetic relationships among nuclear genome types, they were mainly divided into eight groups, A, B1, B2, C1, C2, D1, D2 and E. These results were compared with previous isozyme analysis and RFLP analysis on chloroplast genome using the same varieties. Classification on isozyme analysis matches well with that on nuclear genome, indicating synchronous differentiation of isozyme constitutions and nuclear genomes in Asian varieties. Considering the correspondence between them, nuclear genomes were grouped into Indica (A, B1 and B2), intermediate (C1, C2 and D1) and Japonica (D2 and E) types. From the comparison of chloroplast with nucleus for genome differentiation, two major chloroplast genomes (types 1 and 3) were found in the varieties with several nuclear genome types. However, Japonica group with D2 and E nuclear genomes has only type 1 chloroplast genome, whereas Indica and intermediate groups contain both two major chloroplast genomes. Especially, type 3 chloroplast genome which was not found in Japonica group is dominant type in Indica varieties. The results indicate the differentiation of nuclear genome has partially synchronized with that of chloroplast genome.