Special Considerations in Linkage Analysis

In the preceding chapters, we discussed linkage analysis for a single controlled cross derived from inbred lines or outbred lines. We described a general framework for performing linkage analysis with any type of marker, fully or partially informative, that is qualitatively scored on the presence or absence of a DNA band for an allele. For an outbred cross, the procedure was given to simultaneously estimate the linkage, parental diplotype, and gene order. However, there are many situations in practice in which the strategies for linkage analysis described thus far cannot be appropriately used. In this chapter, we will consider two important issues that have been common or are becoming increasingly common in linkage analysis. The first concerns linkage analysis in a complicated nuclear pedigree, whereas the second deals with linkage analysis based on quantitative marker information.