Abstract: The objective of this study is to analyze the genetic diversity,genetic structure and genetic relationships among japonica rice varieties from different breeding organizations of Yunnan province,and to provide genetic basis for breeding japonica rice varieties. The genetic diversity,genetic structure and cluster analysis of 163 japonica rice varieties from 7 breeding organizations（Geographic regions）of Yunnan province were conducted using 30 pairs of polymorphic SSR markers. The total number of alleles detected from all tested 163 accessions was 207,and the alleles per locus ranged from 2 to 17 with the mean value of 6.6. The index of gene diversity varied from 0.024 4 to 0.823 9 with an average of 0.479 8. The polymorphism information content（PIC）changed from 0.024 1 to 0.802 5 with the average of 0.440 7. The dendrogram of japonica rice varieties was constructed based on Nei’s genetic distance,showed that all rice varieties were subdivided into 4 clusters. The genetic structure analysis was performed based on model,and the varieties of japonica rice were classified into 2 subgroups. The varieties from the Dali Academy of Agricultural Sciences and the Baoshan Academy of Agricultural Sciences were all in the first subgroup,and the varieties of Yunnan Academy of Agricultural Science and Agricultural Scientific Promotion Institute of Chuxiong Yi Autonomous Prefecture were mainly concentrated in the second subgroup. The varieties from Lijiang Academy of Agricultural Science and Qujing Academy Agricultural Sciences were evenly in the two subgroups. It was concluded that the rice varieties in one breeding organization had closer genetic relationship with each other and the genetic diversity in Yunnan province was not rich at present. The genetic relationship among japonica rice varieties was partly correlated with the geographical distribution. The rich japonica rice resources have not been fully exploited yet in Yunnan province.

Key words: japonica rice, SSR markers, genetic diversity, genetic structure