In molecular marker development for genotyping a mapping population, SNPs are easily and often converted to CAPS markers. Can the same be done using InDels? i.e. can InDels be converted to CAPS markers? What is the approach to achieve this?
We use 1bp Indel for marker PCR. It needs an equipment for detecting 1bp DNA length.
Almost any sequence can be turned into a restriction site with the change of 2 bases. The first is supplied by the polymorphism ( a deletion /insertion changes the adjacent base to 2 or 3 constant bases) so you can use primers with a deliberate mismatched base elsewhere to create a restriction site which can only exist in the presence or absence of the expected indel base. You get a feel for how dcaps primers are designed here
http://helix.wustl.edu/dcaps/dcaps.html
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