As sequencing methodology has become ever more rapid, it is becoming reasonable to map by sequencing, thus providing a physical reality to the mutation order. On the other hand, while mapping itself is becoming less relevant, the concept of linkage remains important and will be the focus of this section of the text. It is important to understand the difference between mapping and complementation. Complementation is a test of function. It asks the question if two separate regions of DNA can supply all required functions for an apparently wild-type phenotype.
Mapping is a test of sequence.
Complementation is therefore best analyzed in the absence of recombination while mapping typically demands recombinational events. Your mapping analyses have to be so devised that you can select for a phenotype that requires one or more recombinational events. A term that is used with great frequency in discussions of mapping is linkage . Genetic mapping also makes the assumption that there is only one piece of DNA exchanged between the two organisms. If one utilizes a gene transfer system where more than one distinct piece of DNA can enter the same cell, one of the assumptions used in mapping is violated and problems in interpretation can occur since the apparent linkage would reflect the frequency of the two markers entering the same cell separately and not the genetic distance between them.