Standardization and conversion of marker polymorphism measures

Large scale gene mapping efforts in domestic animals have generated and map ped a large number of genetic markers that are useful for mapping quantitat ive trait and disease loci and for DNA diagnostic purposes such as parentag e testing. Marker polymorphism is an important criterion for selecting gene tic markers in planning experiment for mapping quantitative trait loci or f or DNA diagnostic purposes. Current formulations of marker polymorphism mea sures are functions of marker allele frequencies. In this study, two measur es of marker polymorphism that are available from gene mapping studies and do not require allele frequencies were proposed and analyzed: the observed polymorphic information content (PIC) and the observed family information c ontent (FIC). The observed FIC was more stable than the observed PIC becaus e the observed FIC is unaffected by the variation in the frequency of heter ozygous parents. However, both FIC and PIC are dependent on the gene mappin g design. The effective number of alleles is recommended as a tool to stand ardize marker polymorphism measures so that polymorphism of different marke rs can be compared on an qual basis, and to obtain a new polymorphism measu re (such an exclusion probability) from an existing measure (such as FIC). The usage of the effective number of alleles to standardize MC, PIC and exc lusion probabilities is illustrated using genetic markers in a published li nkage map.