I want to design primers to amplify a gene in genome specific manner in wheat which is present in all A, B and D genomes with high similarity. Because of the high similarity, facing problem in designing in genome specific primers.
I have no idea about the genome of wheat, but for any primer design you can use allele specific primers - these primers are very specific to the alleles, and this assay can help in identification of alleles. This assay will be based on using stringent conditions while running the PCR cycles. Please elaborate your question so that I can answer more specifically.
Would the creation of SNP markers be useful in this case? Maybe making a QTL map and looking at possible markers on those three chromosomes?
you might take a look to this
http://www.ncbi.nlm.nih.gov/pubmed/20497560
In addition to the suggestions of my colleagues, once designed the primers I suggest confirm the specific chromosome amplification using DNA from nulli-tetrasomic.
Check out this: A web tool for Genome Specific Primers design in polyploid species
http://probes.pw.usda.gov/GSP/
Thank you all for the valuable suggestions. Junli Zhang suggested GSP: A web tool for Genome Specific Primers design in polyploid species. This tool suggests various genome specific primer combinations based on variations between the sequences. Its not only suggests better primers and also saves lot of time. I have designed primers using this tool and going to check them. Thanks again.
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