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Inter simple sequence repeat (ISSR) analysis was applied to samples of foxtail millet and its wild ancestor and other close relatives of the genus Setaria in order to detect domestication-related geographical structure and phylogenetic relationship of those species.Eighty-one accessions of nine Setaria species that originated from different regions were used in this study.Fourteen out of the 27 ISSR primers screened amplified successfully and a total of 156 markers were scored for all the accessions,with a high level of polymorphism being detected.The dendrogram based on UPGMA cluster analysis showed clear geographic structure among foxtail millet and its wild ancestor green foxtail,which implies that northern China is the domestication center for both the Chinese and European foxtail millet landraces used in this study.This result did not support the hypothesis that China and Europe are independent domestication centers for foxtail millet proposed by several previous studies based on morphological and isozyme data.The dendrogram also clearly classified the Setaria sample used into two groups,a viridis and a pumila groups.The viridis group was composed of S.viridis,S.italica,S.faberii,S.verticillata,S.leucopila,and S.queenslandica,and the pumila group consisted of S.parviflora and S.pumila,which is consistent with the recently proposed hypothesis of multiple origin of Setaria species.The phylogenetic relationships among different species are discussed.