I need to develop KASP genotyping assay to identify True crosses/F1s in Soybean. I have numerous SNP markers that are polymorphic between the parents. But I am struggling to select the markers from them. Is there any criteria to select the markers that would be used finally in the Assay?
I'd start by using ones that have already been published (if possible). Test them yourself to be sure they work they way you want.
Here's a list of publications to get you started.
https://www.ncbi.nlm.nih.gov/pubmed/?term=KASP%2C+soybean
you can genotype up to 7 snps in a single test using Taqman. you can order the probes with primers directly with them (Thermofischer). you just need to know the SNPs region and what are they. Thermosfischer has very good technical support that can help you with this.
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