Primer design is a crucial step for your assay. The main considerations are:

1. Specificity and minimal selfcomplementarity. LCGreen Plus+ is not a selective DNA dye therefore an unspecific amplification should be avoided.
2. Small PCR product. The resolution of HRMA increases with a decrease of PCR products size. Design your primers to catch 50-80 bp product with SNP in the middle. You can use PCR product of bigger size (up to 400 bp) but than find the region with >2 SNPs. In theory, HRMA can nicely work with 400 bp and one SNP. However most likely you use “dirty” DNA extraction method and contaminants present in the DNA can influence readouts of HRMA.
3. Software. In principle, any program can be used for an optimal primer design. For instance, usually Primer3 gives acceptable primer sets. Annealing temperature in the optimized assay will be approximately 8°C higher than in PCR with home-brew Taq enzyme. The LightScanner® is supplied with a software for the primer design. The software contains a module for the design of LUNA® probes (unlabeled probes, 3′-end is blocked with phosphate group). However in the current version this module does not give an appropriate probes. When a new version will be available we will send a notification mail.
4. Preferably, design 2 primer sets per assay. One primer set can work better than another one.

The guide for the primer design software is available with the software, near the LightScanner® PC and here.Please note that many markers are already designed. You can check list of optimized assays or standard markers for Arabidopsis. The files are updated every week.