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We analyzed length polymorphisms of 377 simple sequence repeat (SSR) markers in 87 cultivated or wild soybeans, including Japanese elite cultivars and irreplaceable genetic resources. The average number of SSR markers in the 20 linkage groups was 18.9, with a range of 13 to 25. All SSR markers showed polymorphism on agarose gel electrophoresis, which revealed 1380 alleles for all accessions. The number of alleles at each locus ranged from 2 to 10, with an average of 3.7, and the polymorphic information content of each marker ranged from 0.02 to 0.86, with a mean of 0.44. Cluster analysis separated the accessions into three clusters. Most Japanese cultivars were found in cluster 1, which was further divided into three subclusters that corresponded to the geographic origin of the cultivars. Most foreign cultivars and all wild accessions were present in clusters 2 and 3, respectively. Our data on the polymorphism of these SSR loci should facilitate the genetic mapping of agronomically important traits and the choice of appropriate markers for marker-assisted selection in soybean breeding programs in Japan.

Genetic diversity of cultivated and wild soybeans including Japanese elite cultivars as revealed by length polymorphism of SSR markers