hello every body
i want to design primer for my sequences but because of cross-pollination nature of my plants (Thymus sp) my sequences are heterozygot (they have SNP). I tried to design primer with primer design software but best recognized primers are in the heterozygot area (they contain SNP), So what can I do?
best regards
you could do an alignment of the two sequences, and design the primer in an homologous zone... you need to know the expression of the gene in question no matter the alele right?
I think it is better to explain my problem more. I have two species with 8 sequences for 4 genes. i know how to design primer for real time-PCR but my problem is I have two species with hetreozygote allele and best rated primers are in hot-spot regions. How could I resolve this problem? On the other hand I don't like other regions because of primer dimer.
You can use high-resolution melt curve based genotyping. Lots of publications on the subject.
https://www.ncbi.nlm.nih.gov/pubmed/?term=high+resolution+melt+curve+genotype
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