Abstract:In order to provide molecular basis for the effective utilization of germplasm resources, the genetic diversity and cluster analysis of 62 indica rice parents from Southeast Asia were discussed by 29 functional gene markers reported as well as 72 conventional SSR markers with rich polymorphism, clear band pattern, and well-distributed in 12 chromosomes. The results showed that 6 functional markers and 26 SSR markers were polymorphic, the percentage of polymorphic loci was 20.7% and 36.1%, respectively. The total number of alleles were 201 and averaged 6.281 per locus with a range from 2 to 12. The number of effective (Ne) ranged from 1.067 to 5.399 with a mean value of 2.867. The polymorphism information content (PIC) ranged from 0.061 to 0.789 with a mean value of 0.515. The Shannon’s information (I) indices varied from 0.143 to 1.908 with an average value of 1.176. The observed heterozygosity (Ho) ranged from 0.936 to 1.000 with an average value of 0.977. The expected heterozygosities (He) ranged from 0.179 to 0.937 with an average of 0.439. UPGMA clustering analysis showed that the 62 indica rice parents from southeast asia could be divided into six groups at a genetic similarity coefficient of 0.805, most of materials from the same country were organized into a big or small category. Compared to the conventional molecular markers, the average number of alleles per locus and the genetic diversity parameter values of functional gene markers was lower. Rice varieties from different countries had a close genetic relationship and a deficiency of genetic diversity, it was indispensable to broaden the genetic basis of rice varieties from southeast asia. The results would provide a scientific evidence for parents selection, creating new germplasm resources and exploitation of heterosis in rice breeding.