General Overview

QTL Cartographer is a suite of programs for mapping quantitative trait loci (QTLs) onto a genetic linkage map. The general experimental paradigm begins with a pair of inbred parental lines that differ in the trait of interest and in the set of marker genotypes. The programs use linear regression, interval mapping [Lander and BotsteinLander and Botstein1989], composite interval mapping [ZengZeng1993,ZengZeng1994] and multiple interval mapping [Kao and ZengKao and Zeng1997,Kao, Zeng, and TeasdaleKao et al.1999,Zeng, Kao, and BastenZeng et al.1999] methods to dissect the underlying genetics of the quantitative traits. Mapping is done onto a set of linked genetic markers with known recombination frequencies. Genetic linkage maps and data files can be imported from Mapmaker/EXP landeretal@87. The mapping program uses a dynamic algorithm that allows a host of statistical models to be fitted and compared, including various gene actions (additive and dominance), QTL-environment interactions, and close linkage.

This package consists of several programs written in C to perform various tasks, including simulating, reformatting or analyzing data and visualizing the results of the analyses. Presently, the mapping programs can handle data from backcrosses, intercrosses and recombinant inbreds, as well as a few other experimental designs (see Table 1.1).

All input and output files are plain text and can be viewed or imported into many text editors and graphics packages on various computing platforms. The programs were originally written for the UNIX operating system and have since been ported to the Macintosh and Microsoft Windows operating systems. Present development is on a Macintosh using Metroworks Codewarrior, which produces binaries for both the Macintosh and Windows operation systems. The UNIX distribution is of the source code and must be compiled at the user's site. This project is ongoing and suggestions are welcome for further improvements and enhancements. The source code and compiled binaries are freely available and may be obtained by anyone over the internet.