Introduction

There are two stages to making a QTL map for a particular trait (once you've scored tens or hundreds of marker loci in tens or hundreds of $F_2$ or backcross progeny):

1. Construct a genetic map of your markers.

2. Feed the genetic map, marker data, and phenotype data into QTL Cartographer and run the analysis.

Although constructing the genetic map of your markers is really important step, we're not going to talk about it further. It is, after all, simply an elaboration of classical Mendelian genetics.¹ We're going to focus on the second step.