Testing for Linkage with a Single Marker

Abstract

In this chapter we introduce the basic principles behind testing a genetic marker for linkage to a quantitative phenotype. We split the presentation into two parts. In the first part we deal with the case of a marker located at a quantitative trait locus (QTL). The parameters that determine the statistical properties of the test are the parameters of the regression model that relates the observed phenotype to the QTL as presented in Chap. 2. Later in this chapter we extend the investigation to the case of a marker in the vicinity of, but not necessarily on top of, the QTL, so the recombination fraction also plays a role. Fortunately the effect of recombination can be separated from the effect of the QTL. From Chaps. 5 onward we discuss the case, which is the common practice today, of testing a set of markers for linkage.