Choice of Marker Loci

Genetic drift will cause a change in gene (allele) frequency at loci, which are segregating within a colony, but is unable to change the frequency of "background" loci, which are fixed (i.e., the frequency of an allele is 100%). However, genetic contamination may introduce new alleles at such loci as well as changing frequency at segregating loci. Thus, some genetic markers can be chosen for nonsegregating background loci that will be sensitive to genetic contamination (taking into account other stocks in the animal house) or could be used to differentiate the stock from other stocks with the same name, and some for loci that are segregating to pick up drift and contamination. One strategy could be to do an initial survey of about 30 to 50 animals using about 20 or more genetic markers, and pick about four or five unlinked and apparently invariant background markers and four or five unlinked segregating markers for routine work. Segregating markers could be chosen that, as far as possible, had about 50% of heterozygous animals (i.e., with two bands) and 50% homozygous animals (i.e., one band), assuming that such markers can be found. If not, markers with the highest proportion of heterozygotes should be chosen. This should overcome the problem of trying to classify multiple alleles, as it is relatively easy to distinguish between one and two bands. In the absence of genetic drift, mutation, directional selection, or contamination, the frequency of heterozygotes should stay constant, according to the Hardy-Weinberg equilibrium, subject to sampling variation.

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