Background/Question/Methods Traditional agricultural systems not only contribute to the food and livelihood security for people throughout the world, but also have maintained a rich diversity of genetic resources, which plays an important role in crop production stability and crop breeding. Underlying mechanism how traditional agricultural systems maintained an abundant diversity would help to design modern sustainable agriculture. The "rice-fish-duck" system, listed as a Globally Important Agricultural Heritage Systems (GIAHS) in 2011, has been widely practiced by local farmers in Congjiang county (108.68E, 25.63N) of Guizhou, China for more than 1200 years. In this study, we collected 113 local rice varieties from 13 natural villages in Congjiang county. We used the molecular methods to analyze the genetic diversity and genetic structure of these local rice varieties. Fifteen pairs of microsatellite primers were used in the molecular analysis. Parameters including number of alleles (Na), number of effective alleles(Ne), Shannon’s diversity index and expected heterozygosity(He) were used to evaluated genetic diversity. AMOVA analysis was also conducted in this study. Results/Conclusions SSR analysis showed that the percentage of polymorphic loci was 100%. A total of 109 alleles were detected, ranging from 2 to 21 alleles per locus and the average number of alleles was 7.3. The average number of effective alleles was 2.902. The genetic diversity index ranged from 0.577 to 2.176, and the average diversity index was 1.184. The average expected heterozygosity was 0.592. By using non-spatial Bayesian cluster procedure in STRUCTURE, there were four genetic groups in Congjiang rice local varieties, and no relatively independent genetic structure was formed among the groups (natural villages). AMOVA analysis showed that 95% of the genetic variation came from within the population. Mantel test showed that the correlation between geographical distance and genetic distance was not significant, indicating that the population structure in this area is subject to the "IBD" model and the population gene flow is limited by geographic isolation. These results suggested that high genetic diversity in local rice varieties was maintained in the traditional rice-fish-duck system.
