| Summary: | As an important driving force, introgression plays an essential role in shaping the evolution of plant species. However, knowledge concerning how introgression affects plant evolution in agroecosystems with strong human influences is still limited. To generate such knowledge, we used InDel (insertion/deletion) molecular fingerprints to determine the level of introgression from <i>japonica</i> rice cultivars into the <i>indica</i> type of weedy rice. We also analyzed the impact of crop-to-weed introgression on the genetic differentiation and diversity of weedy rice, using InDel (insertion/deletion) and SSR (simple sequence repeat) molecular fingerprints. Results based on the STRUCTURE analysis indicated an evident admixture of some weedy rice samples with <i>indica</i> and <i>japonica</i> components, suggesting different levels of introgression from <i>japonica</i> rice cultivars to the <i>indica</i> type of weedy rice. The principal coordinate analyses indicated <i>indica</i>–<i>japonica</i> genetic differentiation among weedy rice samples, which was positively correlated with the introgression of <i>japonica</i>-specific alleles from the rice cultivars. In addition, increased crop-to-weed introgression formed a parabola pattern of dynamic genetic diversity in weedy rice. Our findings based on this case study provide evidence that human activities, such as the frequent change in crop varieties, can strongly influence weed evolution by altering genetic differentiation and genetic diversity through crop–weed introgression in agroecosystems.
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