Modified High-Resolution Melting (HRM) Marker Systems Increasing Discriminability Between Homozygous Alleles

Targeted single-nucleotide polymorphism (SNP) genotyping, especially for functional nucleotide polymorphism, is widely used for current breeding programs in crops. One of the cost- and time-effective approaches for genotyping is high-resolution melting (HRM) analysis for polymerase chain reaction (PCR) amplicons, including target SNP. The reliability of a genotype obtained from an HRM marker depends on the difference in Tm values between two amplicons. Increasing the reliability of HRM marker genotypes could be archived with the selection of the best nearest neighboring nucleotide substitution (NNNs) in primer sequences surrounding SNPs. This chapter provides an easy-way protocol to design primer sequences for NNNs-HRM markers with table and web service, as well as several tips to develop HRM markers that distinguish between homozygous alleles (e.g., between A/A and C/C).