Association between a genetic trait and a marker: discrimination between epistasis and gametic disequilibrium

We reconsider the method of Ott and Falk (1982) for the analysis of genetic linkage and of epistasis in the presence of phenotypic association. Their approach is extended to allow for gametic disequilibrium between marker and trait loci. We show that epistasis and tight linkage with gametic disequilibrium may be indistinguishable as explanations of association even in a very large pedigree.