Alternative explanation on marker conversion
Marker conversion is changing markers that are unreliable, technically difficult to operate, or not polymorphic between a new pair of parents. They are converted into reliable markers that are simple to operate and relatively cheap.
To create a linkage map, the first aim is to get as many closely linked markers as possible. In this process, also markers are used that are expensive and complicated to use. For marker-assisted breeding, two flanking markers per gene may be sufficient and because of the scale of use, it is important that the operation of this marker is simple, reliable and cheap. Therefore, markers that are poorly reproducible (like RAPDs), relatively expensive and/or relatively difficult to operate (like for instance AFLP markers or CAPS markers that require an additional digestion step) have to be converted to markers that can be run at high throughput, such as SNPs.