ABSTRACT
The huge number of publications in the area of quantitative trait loci (QTL) detection by far exceeds the number of reported applications, which in turn, greatly exceeds the number of QTL identified and actually utilized in animal improvement programs. Thus, the presumption that marker and QTL alleles are in linkage equilibrium should probably be made as a conservative basis for QTL mapping in livestock. Human and animal geneticists have access to data structures that are defined by multigenerational families and marker-QTL phase relationships that differ among the families due to the population level linkage equilibrium. Penrose defined the “reference structure” in which marker and QTL alleles are in linkage disequilibrium to be a family of sibs. QTL analysis in human genetics extends well beyond the sib-pairing approaches. However, if a QTL is linked to the marker, the divergent selection should result in considerable marker allele frequency differences between the tails, which can be detected by several statistical methodologies.
