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Setaria viridis (L.) Beauv., or green foxtail, is native to Eurasia and is the putative ancestor of foxtail millet. Due to the advantageous genetic characteristics of S. viridis, it is a model species for C4 plants. However, S. viridis has seriously spread to the agricultural system around the world because of its wide adaptability. This study is aimed to understand the distribution of S. viridis in Taiwan, and also to investigate the genetic diversity and relationships among different wild populations. A total of 141 S. viridis collected at 10 sites with sampling sizes ranging from 8 to 24 plants in Taiwan were analyzed by 13 highly polymorphic SSR markers, and 6.1 alleles per locus were detected in our study. The relationships of collected S. viridis mostly corresponded to its distribution in different parts of Taiwan revealed by PCoA and phylogenetic tree. Similarly, the results for population structure showed the significance of collecting site or geographical factors. Finally, the extent of gene flow was studied with the genetic differentiation (FST) and Nm values, and two S. viridis populations were found to significantly contain the existence of gene-flow events. In conclusion, S. viridis showed a pattern of low diversity and heterozygosity within a population, but high differentiation among populations because of its selfing attribute and the barriers of sea and mountain range for gene flow. In addition, the founder effect may be the other reason for this pattern of population genetic structure.

High Differentiation among Populations of Green Foxtail, Setaria viridis, in Taiwan and Adjacent Islands Revealed by Microsatellite Markers