Abstract：The japonica rice (Oryza satiua ssp. japonica) resources are rich in Taihu area. Along with large-scale popularization of rice varieties, the genetic basis of breeding material is became narrower and the genetic similarity is increased, thus the japonica rice breeding has became more difficult. Genetic diversity of 42 japonica rice varieties, collected from Taihu area, was analyzed by 24 pairs of simple sequence repeat (SSR) primers. The SSR primers were located at 12 rice chromosomes, and 2 pairs of SSR primers were selected at each chromosome. The results showed that 23 pairs of SSR primers performed polymorphism in the 42 materials. A total of 105 alleles loci were detected among 42 varieties using the 23 pairs of SSR primers. The average number of detected alleles by each primer pair was 4.57 with a range from 2 to 8. The effective alleles were 56.43 with average 2.45. The value of allelic polymorphism information content (PIC) varied widely from 0.083 0 to 0.807 9 with an average value of 0.496 6. The number of polymorphic loci each variety ranged from 6 to 19, and the number of allele loci ranged from 27 to 55. The genetic similarity coefficient of SSR markers among 42 japonica rice varieties ranged from 0.391 to 0.990, with average 0.610, and the genetic similarity coefficient of 74.45% tested materials ranged from 0.50 to 0.80. Furthermore, the UPGMA(unweight pair group method with arithmetic mean) clustering analysis at the genetic similarity value of 0.50 grouped the 42 japonica rice varieties into two groups. The 19 conventional japonica rice varieties could be grouped, and they were divided into 2 subgroups at the level of genetic similarity coefficient 0.58. Another group was composed of the 23 japonica hybrid rice varieties, and it also was divided into two subgroups at the level of genetic similarity coefficient 0.70. Based on the all analysis, it was concluded that the genetic background comparability of the japonica rice varieties in Taihu area was high and the diversity was low. Therefore, introducing and making use of the new genetic resources and creating breeding materials should be strengthened. The genetic diversity of japonica rice based on SSR markers can provide technical support and theoretical basis for breeding new rice varieties in Taihu area.
