3 Photograph of an electrophoresis gel. Vertical lanes represent the genome of individual embryos. First, they have has been stained with ethidium bromide, an intercalating agent, which binds between the two strands of DNA and fluoresces when irradiated with UV light. The fact that each embryo has different markers in its genome accounts for the genetic differences between individuals. Normally, screening markers amplified by 300 randomly chosen primers using BSA yields about 5-10 putative markers.
Putative markers have high probabilities of being linked to the mutation.
RAPD assays of these few markers will tell us if the marker is, in fact, linked to the mutation and give us the genetic distance. Occasionally, these putative markers will prove not to be linked, in which case screening markers amplified by different primers will be required. Because PCR thermocontrollers can test 48 primers per reaction, we need to carry out four reactions to test all primers that amplify mapped markers. If a few putative FPM map in the same chromosome of the genetic linkage map, then we can expect the mutant gene to reside in the same chromosome. Using FPPs and the map accelerates the process of finding the chromosome on which the gene is located.