Plant & Animal Genome IX Conference Plant & Animal Genome IX Conference
Computer: Demonstrations
C01_03.html
Map Manager QTX software analyzes the results of experimental genetic crosses to map Mendelian and quantitative trait loci (QTLs). It is available in versions for both Microsoft Windows and Mac OS operating systems. It uses regression to detect and map QTLs by three methods: association with single marker loci, simple interval mapping, and composite interval mapping. Map Manager QTX was first released in February, 2000 and revisions have been released at monthly intervals since then. Revisions include new functions as well as bug fixes. One important new function is the ability to estimate the genotypes of missing marker data during QTL mapping, using a Markov-chain algorithm described by Jiang and Zeng (Genetica 101: 47-58 (1997)). This improvement makes most data sets more informative and makes Map Manager QTX more equivalent to software which uses maximum-likelihood methods. In addition, Map Manager QTX now supports advanced backcross and advanced intercross designs and a new design called recombinant inbred intercross. Finally, Map Manager QTX now offers weighted regression for QTL mapping with recombinant inbred lines in which an estimate of the trait variance is available for each line. Unlike many other QTL mapping programs, Map Manager QTX automatically calculates a genetic map for marker loci from the marker genotypes. This function works well except for certain crosses, such as advanced backcrosses, in which the marker genotype data is insufficient to define a good map. Map Manager QTX is being extended to allow use of an externally defined marker map.