In silico mapping of 1758 new SSR markers developed from public genomic sequences for sorghum

In order to develop simple sequence repeat (SSR) markers for sorghum, a total of 2,113 primer pairs were designed from 81,342 public genomic sequence contigs of sorghum [methyl-filtered sequences downloaded from SAMI (Sorghum Assembled Genomic Island)]. After screening eight sorghum lines, 1,758 primers amplifying polymorphisms were identified. Of these 1,710 SSR markers were predominantly polymorphic in the eight lines and could detect from two to eight alleles. In addition, 1,692 of the markers were mapped on to the ten sorghum chromosomes by in silico mapping. The number of markers per chromosome ranged from 107 to 285. These SSR markers will provide an ideal marker system to help with gene targeting, gene cloning, quantitative trait locus mapping, and marker-assisted selection in sorghum species.