this work was supported by a grant from the ministry of agriculture , forestry and fisheries of japan ( genomics for agricultural innovation , sor 0006 ) .
simple sequence repeat ( ssr ) markers with a high degree of polymorphism contribute to the molecular dissection of agriculturally important traits in sorghum ( sorghum bicolor ( l. ) moench ) . 
 we designed 5599 non - redundant ssr markers , including regions flanking the ssrs , in whole - genome shotgun sequences of sorghum line atx623 . 
 ( at / ta)n repeats constituted 26.1% of all ssrs , followed by ( ag / tc)n at 20.5% , ( ac / tg)n at 13.7% and ( cg / gc)n at 11.8% . 
 the chromosomal locations of 5012 ssr markers were determined by comparing the locations identified by means of electronic pcr with the predicted positions of 34 008 gene loci . 
 most ssr markers had a similar distribution to the gene loci . among 970 markers validated by fragment analysis , 67.8% ( 658 of 970 ) markers successfully provided pcr amplification in sorghum line btx623 , with a mean polymorphism rate of 45.1% ( 297 of 658 ) for all ssr loci in combinations of 11 sorghum lines and one sudangrass ( sorghum sudanense ( piper ) stapf ) line . 
 the product of 5012 and 0.678 suggests that 3400 ssr markers could be used to detect ssr polymorphisms and that more than 1500 ( 45.1% of 3400 ) markers could reveal ssr polymorphisms in combinations of sorghum lines .