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A caution: the marker does not (usually) equal the gene

Except in cases where DNA sequence and specific gene location is known, a marker is located near, but not within, the gene of interest. It may not be known how close the marker is to the actual gene. Every cross that is made gives a chance that recombination will occur in the region in between the marker and the gene, and some progeny may no longer have the desired allele of that gene even though the correct marker allele is present.

This can be mitigated by:

•Using a marker that is very tightly linked (having a very small distance between the marker and the gene of interest)
•Using 2 markers flanking the gene of interest
•Fine mapping to find markers that exactly identify the gene or are very close