ABSTRACT
In this chapter, the authors determine linkage between marker loci and quantitative trait loci (QTL) and for determining map location of QTL and their genetic effects in animal populations are presented. Marker-QTL linkage analyses will often involve a large matrix consisting of many markers tested against a number of traits. Since markers will exhibit linkage with one another and traits may be correlated to a greater or lesser extent, determining appropriate levels of statistical significance for the entire matrix of results is a problem. Populations of agricultural animals invariably reproduce by cross-fertilization. For such populations, the particular source of linkage disequilibrium utilized for marker-QTL mapping will depend on the genetic history of the trait and populations involved. Maximum-likelihood methods can readily be applied to analysis of marker-QTL linkage in the offspring of a single sire.
