Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus (A) ranging from 2 to 18 (average 10.6), and polymorphic loci (P) from 40.0% to 100% (average 83.3%). The observed heterozygosity (H-O) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity (H-E) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found (R-ST = 0.5199, theta = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise theta) was positively correlated with geographical distance (r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.