Additional file 4.

Population structure analysis plots with three K values (K = 2, 3, 4) using STRUCTURE program [54]. The top panel (K = 2) showed that Japanese cultivars were divided by 192 SNP genotypes of Nipponbare (Red arrow) and Koshihikari (Green arrow). This is natural result because all SNPs tested were extracted from the mapping result of Koshihikari short sequences to Nipponbare genome. The other panels show the relatively same population size of Koshihikari SNP group, but with further population subdivision within the Nipponbare SNP group from K = 3. All panels (K = 2, 3, 4) indicate that population structure was not associated with the year each cultivar released.

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Yamamoto et al. BMC Genomics 2010 11:267   doi:10.1186/1471-2164-11-267