Simple Sequence Repeat (SSR) DNA markers or Microsatellites are di-, tri-, tetra-nucleotide tandem repeats containing loci of eukaryotic genomes. It is demonstrated that these loci are very polymorphic due to the change in the number of repeating units among the individuals of populations. Each SSR locus can easily be amplified by using a polymerase chain reaction (PCR) knowing the DNA sequence flanking the repeat region specifically. The only limiting feature of the application of these markers is the need for prior sequence information for developing primers in locus-specific PCR amplification. This limitation is alleviated for the economically important species and the ones closely related, since primer sequences of the SSR DNA markers and the amplification conditions are available in the literature. However, when the reported PCR amplification conditions were applied, with the 2 wheat SSR markers, we found that contaminating bands appeared on the gels. This is most likely due to different laboratory conditions. In this study, we report the optimization of PCR conditions for WMS30 and WMS46 of wheat. The most important parameters were found to be the annealing temperature and Mg2+ ion concentrations.

Simple Sequence Repeat (SSR) DNA markers or Microsatellites are di-, tri-, tetra-nucleotide tandem repeats containing loci of eukaryotic genomes. It is demonstrated that these loci are very polymorphic due to the change in the number of repeating units among the individuals of populations. Each SSR locus can easily be amplified by using a polymerase chain reaction (PCR) knowing the DNA sequence flanking the repeat region specifically. The only limiting feature of the application of these markers is the need for prior sequence information for developing primers in locus-specific PCR amplification. This limitation is alleviated for the economically important species and the ones closely related, since primer sequences of the SSR DNA markers and the amplification conditions are available in the literature. However, when the reported PCR amplification conditions were applied, with the 2 wheat SSR markers, we found that contaminating bands appeared on the gels. This is most likely due to different laboratory conditions. In this study, we report the optimization of PCR conditions for WMS30 and WMS46 of wheat. The most important parameters were found to be the annealing temperature and Mg2+ ion concentrations.