QTL are quantitative trait loci: genetic loci that contribute to variation in
a quantitative trait. QTL mapping is the effort to identify QTL through an
experimental cross.
In this book, we give an overview of the practical aspects of the analysis
of QTL mapping experiments based on inbred line crosses, with explicit instructions
on the use of the R/qtl software (an add-on package for the general
statistical software, R). We give some of the details of the statistical methods,
but we mostly focus on how to get and make sense of results. Real data
examples are included throughout.
The intended audience includes scientists who are performing QTL mapping
experiments and participating directly in the analysis. We expect the
reader to have a general understanding of statistical methods, including maximum
likelihood estimation and linear regression. Some readers will be statisticians
analyzing data from QTL experiments with a basic understanding of
genetics. We provide limited introduction to either statistics or genetics. Readers
with a limited understanding of statistics may wish to first study Rice
(2006). Readers with a limited understanding of genetics may wish to first
study Brown (2006). Alternatively, one might consider The Cartoon Guide
to Statistics (Gonick and Smith, 1993) and The Cartoon Guide to Genetics
(Gonick and Wheelis, 1991), which are more gentle and entertaining (but less
complete) introductions to the subjects.