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The molecular evolution of cultivated rice  Oryza sativa  L. has long been a subject of rice evolutionists. To investigate genetic diversity within and differentiation between the  indica  and  japonica  subspecies, 22 accessions of  indica  and 35 of  japonica  rice were examined by five microsatellite loci from each chromosome totalling 60 loci. Mean gene diversity value in the  indica  rice ( H =0·678) was 1·18 times larger than in the  japonica  rice ( H =0·574). Taking the sampling effect into consideration, average allele number in the  indica  rice was 1·40 times higher than that in the  japonica  rice (14·6 vs 10·4 per variety). Chromosome-based comparisons revealed that nine chromosomes (1, 2, 3, 4, 5, 8, 9, 10 and 11) harboured higher levels of genetic diversity within the  indica  rice than the  japonica  rice. An overall estimate of  F  ST  was 0·084–0·158, indicating that the differentiation is moderate and 8·4–15·8% of the total genetic variation resided between the  indica  and  japonica  groups. Our chromosome-based comparisons further suggested that the extent of the  indica – japonica  differentiation varied substantially, ranging from 7·62% in chromosome 3 to 28·72% in chromosome 1. Cluster analyses found that most varieties formed merely two clusters for the  indica  and  japonica  varieties, in which two  japonica  varieties and five  indica  varieties were included in the counterpart clusters, respectively. The 12 chromosome-based trees further showed that 57 rice varieties cannot be clearly clustered together into either the  indica  or  japonica  groups, but displayed relatively different clustering patterns. The results suggest that the process of  indica – japonica  differentiation may have proceeded through an extensive contribution by the alleles of the majority in the rice genome.

Microsatellite diversity within Oryza sativa with emphasis on indica–japonica divergence