The locus specific primer will have as its 3' nucleotide a base known to be specific for that homoeologue - and this can be deduced by checking multiple sequence alignments, e.g. as produced by clustal or Cap3.
Similarly, the 3' base of the SNP primers will be the variant nucleotide that determines the SNP.
Ideally the Tms of the primers should be around 60C. When you carry out a PCR with all 3 primers together, if the Tm is too high you will see no amplification, if too low you may see many bands, but no distinction between genotypes. When its just right, you will see only the bands that you expect to see, and with differences apparent between genotypes - band positions shifted by 2 bases (depending which of the 2 SNP primers matched that genotype). In practice we use a touchdown PCR from 60C to 55C anneal, 3 cycles per step down, each step down 1C lower, followed by 30 or so cycles at 55C anneal. I say 30 cycles or so as this procedure always gives us too much product that needs to be diluted - so it will probably end up as 20 cycles or thereabouts.
For an example see here. In this example the alleles are 3 bases different in size.
Just one word of caution, not all Taq polymerases are suitable for this. We have tested the Stoffel fragment and Amplitaq Gold. Amplitaq Gold gave much cleaner results.
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