Plant Genome III Conference Plant Genome III Conference
QTL Cartographer is an interactive computer program package for mapping quantitative trait loci (QTLS) using linear regression, interval mapping [E.S. Lander and D. Botstein, Genetics 63:185-199 (1989)] or composite interval mapping [Z.-B. Zeng, Genetics 136:1457-1468 (1994)] methods. Mapping is done onto a set of linked genetic markers with known recombination frequencies, and this genetic linkage map data can be imported from MapMaker [E.S. Lander, et al, Genomics 1:174-181 (1987)]. The package consists of a suite of programs written in C for simulation studies of backcross and F2 designs and the analysis of either simulated or real data. Other experimental designs can be easily incorporated. The mapping program uses a dynamic algorithm that allows a host of statistical models to be fitted and compared, including various gene actions (additive, dominance and epistasis), QTL-environment interactions, pleiotropic effects and close linkage. The package also implements the simultaneous mapping of multiple traits using the interval or composite interval mapping methods. A 'front end' program manages data files and allows for a menu driven approach to simulation studies and analysis. The results can be displayed graphically, or printed using Gnuplot, or alternatively can be imported into any graphics package on any computing platform. The programs are written for the Unix operating system but the code for most of the programs in the package has been ported to the Macintosh and Microsoft Windows operating systems. The source code and binaries are freely available and may be obtained via anonymous ftp at esssjp.stat.ncsu.edu in the subdirectory /pub/qtlcart.