| Single Nucleotide Polymorphisms (SNPs) is a kind of genetic variation which is the most abundant variation in biological genome and can represent genetic background in truth. Through SNPs frequencies, allele frequencies at SNPs loci, gene frequancies and differentiation at SNPs loci, gene frequancies and differentiation at genome loci, we can clarify the genetic difference between japanica and indica at the DNA level.DNA fragments in 24 loci distributed in each chromosome (18989 bp) were sequenced in the 38 accessions of Chinese Cultivated Rice (Oryza sativa L.) including 20 accessions of japonica and 18 accessions of indica. There were 92 SNPs and 75 haplotype in total. Of 92 SNPs, transitions accounted for 65 (70.6%). Allele frequencies at 65 (70.6%) SNPs loci showed significiant difference between japonica and indica. 11 SNPs at 5 genomic loci can distinguish japonica from indica. 32 and 67 SNPs were found respectively in japonica and indica. The SNPs frequency θ was 0.47, 1.02 SNPs/kb respectively in japonica and indica, and the SNPs frequency π was 0.31×10-3, 1.27×10-3 respectively. Mean differentiation of SNPs at intron region and exon region was lager than the mean differentiation of SNPs at intergene region. 38 and 47 haplotypes were detected in japonica and indica, and 15 common haplotypes. Mean haplotype divergence was 0.14, 0.234 in japonica and indica respectively. Haplotype differentiation (Gst) was beween 0 and 1.From the result above, genetic divergence of japonica was lager than indica. The genetic differentiation between indica and japonica was significant. It showed the complexity of population structure in rice. Furthermore, UPGMA and Bayesian cluster can distinguish indica from japonica. Bayesian cluster can resolve population structure more clearly and observe the admixture of rice effectively.
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