MapQTL is a computer program for the analysis of quantitative trait loci (QTL) in experimental populations of diploid species, in other words for doing QTL analysis. With QTL analysis regions on the genome that are responsible for phenotypic variation in the investigated quantitative trait can be detected and the associated genotypic effects will be estimated. The program can analyse QTL experiments with interval mapping (Lander & Botstein, 1989; Van Ooijen, 1992), with the powerful MQM mapping (Jansen, 1993) (which is equivalent to composite interval mapping (Zeng, 1994)), and with a nonparametric method. MapQTL is an MS-Windows program, it easy to use and is very fast.
<Features> - The Haley & Knott regression approximation to maximum likelihood interval and MQM mapping was added. Advantages of the regression approach are a magnitude higher speed and reduced use of RAM memory, while the quality of the approximation is generally quite good. - Three population types that can be analysed were added: DH2: doubled haploid population drawn from an F2, one doubled gamete from one F2 plant; BCpxFy: advanced backcross inbred line family (any generation); IMxFy: advanced intermated inbred line family (any generation). - Simple experimental design (e.g. blocking) and covariates can be analysed jointly with interval and MQM mapping. - Traits observed in multiple populations can be analysed combined over the populations with interval and MQM mapping based on a common (integrated) linkage map. - intuitive MS-Windows user interface; - many experimental population types: first generation backcross, F2, recombinant inbred lines family, family of F1-derived doubled haploids, family of F2-derived doubled haploids, advanced backcross inbred lines family, advanced intermated inbred lines family and outbreeder full-sib family; - input in plain text files with a flexible layout of the quantitative trait data, the molecular marker genotypes and the (precalculated) linkage map; map and molecular marker data files are compatible with JoinMap; - for an outbreeder full-sib family interval mapping is enhanced to 'all-markers' mapping (Maliepaard & Van Ooijen, 1994), employing the segregation information of all linked markers, each of which may follow a different segregation type, with two up to four alleles (linkage phases must be known); - MQM mapping, in which markers are used as cofactors to absorb the effects of nearby QTLs, thereby increasing the power for mapping other segregating QTLs; it may even enable the separation and mapping of linked QTLs (Van Ooijen, 1994); - automatic selection of cofactors using a backwards elimination procedure to easily get the set of cofactors for MQM mapping; - permutation test to determine the significance level of interval mapping without the usual assumption of normality of the data residuals; - nonparametric mapping with the Kruskal-Wallis rank sum test per marker to assess the segregation of QTLs for non-normally distributed data; - multiple populations and maps in a single project; - analysis results stored in sessions for (re-)inspection; - clearly arranged results, mostly in adjustable and sortable tables; - QTL charts, with many adjustable features; - results and charts exportable to most MS-Windows text processing and presentation software; - print preview; - manual in Adobe PDF format; - easy-to-use InstallShield installer.