Linked quantitative trait loci (QTLs) can arise through normal population genetic processes.

For any given phenotype there are many loci where mutations can have an effect. Different populations will experience mutations in different loci affecting the same phenotype. These mutations can affect a phenotype in a positive (+) or negative (−) way and if nearly neutral ( = ) will remain segregating within a population for awhile. As other mutations occur, advantageous combinations can result with better fitness than either mutation alone or the original parental alleles. Multiple mutations with effects upon a trait will be broken up by recombination if not linked and one or more can therefore be lost. Linked mutations can become fixed as blocks of larger collections of QTLs if the combination of alleles is beneficial. Different populations may evolve different “super”-QTLs, which are revealed when the populations interbreed. Offspring will express a range of phenotypes depending on which QTLs are inherited and how much recombination breaks up the linked groups. Multiple rounds of interbreeding can further break up the linked QTLs revealing individual loci, as illustrated in Figure 2.