Single-QTL analysis

The most commonly used method for QTL analysis is interval mapping, in which one posits the presence of a single QTL and considers each point on a dense grid across the genome, one at a time, as the location of the putative QTL. A central issue concerns the treatment of missing genotype information: at a position between genetic markers, genotype data are not available and must be inferred on the basis of the available marker genotype data. Several methods are available; we describe the most popular. These methods all have analogs for the fit of multiple-QTL models, which will be discussed in Chap.8 and 9. We further discuss the establishment of statistical significance in such single-QTL genome scans, and the special treatment that is required for the X chromosome. But first, in order to introduce the basic ideas in QTL mapping, we describe an even simpler method, sometimes called marker regression.