Abstract: Weedy rice, the same biological species of cultivated rice, is a noxious weed that infests rice fields worldwide. To determine the genetic diversity, structure, and relationships of weedy rice in China, we applied insertion/deletion (InDel) molecular fingerprints to analyze weedy rice populations from northeastern to southern rice planting regions, using japonica and indica rice cultivars as references. The InDel fingerprints indicated relatively high overall genetic diversity (H_e = 0.42) for the 240 samples from 14 weedy rice populations. However, much lower within-population diversity was detected, particularly for populations from northeastern and southern China, with the H_e value ranging from 0.006 to 0.06. Jiangsu populations showed much higher within-population genetic diversity (H_e = 0.12–0.31) than those from other regions. Analysis of molecular variance and F_st showed ∼88% genetic variation among weedy rice populations. Principal component and structure analyses indicated substantial japonica–indica genetic differentiation of weedy rice populations. Weedy rice from Jiangsu province was undergoing indica–japonicadifferentiation even within populations, which was likely due to the replacement of indica by japonica rice varieties in this region. In conclusion, significant genetic divergence has taken place among weedy rice populations in China, which is associated with their geographic locations and coexisting rice varieties. Introgression from cultivated rice has a critical role in shaping the genetic diversity and structure of weedy rice populations in agro-ecosystems influenced by humans.

Key words: adaptive evolution, agro-ecosystem, genetic differentiation, introgression, molecular markers, weed