In the other hand, the primer for SNP detection should be 3 prime end specific. The 3 prime end can design both of forward and reverse primer. It depend on your decision to design which primer will bind to specific allele, either forward or reverse primer. The interesting method to discriminate between different allele is Tetra primer ARMS-PCR.

http://www.biomedcentral.com/1471-2105/9/253/figure/F4?highres=y

In the other hand, the primer for SNP detection should be 3 prime end specific. The 3 prime end can design both of forward and reverse primer. It depend on your decision to design which primer will bind to specific allele, either forward or reverse primer. The interesting method to discriminate between different allele is Tetra primer ARMS-PCR.

http://www.biomedcentral.com/1471-2105/9/253/figure/F4?highres=y

WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

BMC Genomics20078:275

DOI: 10.1186/1471-2164-8-275

Tetra1-ARMS PCR primer designing tool will be useful to design Allele-specific primers.

Best wishes

has anybody tried Tetra-ARMS PCR method for haploid organisms?

facing the same issue

Dear Kallafalla, I managed to make Tetra-ARMS PCR work for me in order to detect a single SNP in the gene just with PCR. The method requires a bit of adjustment of the protocol in the beginning but works consistently after all the adjustments (temperature, concentrations of primers etc.) are made.