Standardization and conversion of marker polymorphism measures

Large scale gene mapping efforts in domestic animals have generated and mapped a large number of genetic markers that are useful for mapping quantitative trait and disease loci and for DNA diagnostic purposes such as parentage testing. Marker polymorphism is an important criterion for selecting genetic markers in planning experiment for mapping quantitative trait loci or for DNA diagnostic purposes. Current formulations of marker polymorphism measures are functions of marker allele frequencies. In this study, two measures 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 content (FIC). The observed FIC was more stable than the observed PIC because the observed FIC is unaffected by the variation in the frequency of heterozygous parents. However, both FIC and PIC are dependent on the gene mapping design. The effective number of alleles is recommended as a tool to standardize marker polymorphism measures so that polymorphism of different markers can be compared on an equal basis, and to obtain a new polymorphism measure (such an exclusion probability) from an existing measure (such as FIC). The usage of the effective number of alleles to standardize FIC, PIC and exclusion probabilities is illustrated using genetic markers in a published linkage map.