YANG DA (1), Paul M. VanRaden (1), Micha Ron (2), Jonathan E. Beever (3), Jiuzhou Song (2), George R. Wiggans (1), Runlin Z. Ma (3), Joel I. Weller (2), and Harris A. Lewin (3)

1. Animal Improvement Programs Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland 20705-2350, USA
2. Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel
3. Department of Animal Sciences, University of Illinois, Urbana, IL 61801

Large-scale gene mapping efforts for domestic animals have generated and mapped a large number of genetic markers, which are useful for parentage testing and mapping quantitative trait and disease loci. Measures of marker informativeness are helpful when selecting genetic markers and can be calculated when allele frequencies are available. However, reliable estimates of allele frequencies may not be available from some gene mapping designs. Thus, two measures of marker informativeness that do not require prior knowledge of allele frequencies were analyzed: the observed polymorphic information content (PIC) and the observed family information content (FIC), which was defined as the expected frequency of offspring that can identify parental allele transmission unequivocally per heterozygous parent. The FIC was found to be more stable than PIC. Both measures were standardized to account for different genotyping schemes. Effective number of alleles was defined as the required number of alleles with equal allele frequency to achieve the observed FIC. This measure was found to be the most appropriate criterion to measure the degree of polymorphism of 247 microsatellite genetic markers analyzed in half-sib families. The effective number of alleles is independent of the experimental design and can be used to derive standardized estimates of heterozygosity, PIC, and exclusion probability.