MapQTL ® 6
Software for the mapping of quantitative trait loci in experimental populations of diploid species
Analyse your QTL experiments with interval mapping, with the powerful MQM mapping (=composite interval mapping), or with a nonparametric method. MapQTL is easy to use, is very fast and presents the analysis results in tables and (adjustable) charts, that can be exported to MS-Windows ® text processing and presentation software.
New features of version 6
- 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.
Get an impression of the software with the slide show:
MapQTL 6 slide show (size: ~0.9 MB).
User-friendly power in QTL analysis
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.
The general concept of the program is the following. As a first step prepared data files of the marker observations, of the quantitative trait observations and of the genetic linkage map are loaded into what is called a project, which is just a working area for the program. These three input files are in a relatively simple plain text format. The map must be precalculated with computer software for genetic linkage mapping, such as JoinMap ® (Van Ooijen, 2006) or MAPMAKER (Lander et al, 1987). Next, the trait to be analysed for segregating QTLs must be selected with a mouse click in the graphical user interface (or with the keyboard), similarly the map and linkage groups to be used must be selected, the type of analysis must be chosen, various other computational parameters may be modified to your preference and subsequently the analysis can be run. After each successfully performed analysis the results are stored in so-called sessions that can be inspected right away and that will remain available for inspection any time later. The analysis results are presented in clearly arranged tables and highly customizable charts. These can be exported to files and copied to most MS-Windows text processing, presentation and spreadsheet software.
The present version 6 has several important new features with respect to its predecessor version 5 (Van Ooijen, 2004). A major one is the regression approximation to maximum likelihood interval and MQM mapping. The regression approach to interval mapping was introduced by Haley & Knott (1992) and independently also by Martínez & Curnow (1992). 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 (c.f. Haley et al, 1994; Knott et al, 1996; Knott et al, 1998; Kao, 2000). To the already large list of population types that can be analysed three more were added: a family of F2-derived doubled haploid lines, a family of advanced backcross inbred lines and a family of advanced intermated inbred lines. Another added feature is the possibility to analyse simple experimental design (e.g. blocking) and covariates jointly with interval and MQM mapping, which may increase the power and precision of the QTL analyses. Finally, 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.
MapQTL 6 is available as 32-bit software for the 32- and 64-bit MS-Windows 10 platform. Other MS-Windows platforms are not supported. Previous versions are no longer available.
- The first version of MapQTL available to the public was version 3.0. It was presented at the Plant Genome IV Conference, January 1996, San Diego, California, USA (Van Ooijen & Maliepaard, 1996).
- MapQTL 4.0 was presented at the Plant & Animal Genome VIII Conference, January 2000.
- MapQTL 5 was presented at the Plant & Animal Genome XII Conference, January 2004.
- The current version was presented at the Plant & Animal Genome XVII Conference, January 2009.
- Haley & Knott, 1992. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324.
- Haley, Knott & Elsen, 1994. Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136: 1195-1207.
- Jansen, 1993. Interval mapping of multiple quantitative trait loci. Genetics 135: 205-211.
- Kao, 2000. On the differences between maximum likelihood and regression interval mapping in the analysis of quantitative trait loci. Genetics 156: 855-865.
- Knott, Elsen & Haley, 1996. Methods for multiple-marker mapping of quantitative trait loci in half-sib populations. Theor. Appl. Genet. 93: 71-80.
- Knott, Marklund, Haley, Anderson, Davies, Ellegren, Fredholm, Hanson, Hoyheim, Lundstrom, Moller & Anderson, 1998. Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics 149: 1069-1080.
- Lander, Green, Abrahamson, Barlow, Daly, Lincoln & Newburg, 1987. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.
- Lander & Botstein, 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
- Maliepaard & Van Ooijen, 1994. QTL mapping in a full-sib family of an outcrossing species. In: [Van Ooijen & Jansen (eds), 1994]: 140-146.
- Martínez & Curnow, 1992. Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theor. Appl. Genet. 85: 480-488.
- Van Ooijen, 1992. Accuracy of mapping quantitative trait loci in autogamous species. Theor. Appl. Genet. 84: 803-811.
- Van Ooijen, 1994. Comparison of a single-QTL model with an approximate multiple-QTL model for QTL mapping. In: [Van Ooijen & Jansen (eds), 1994]: 205-212.
- Van Ooijen, 2004. MapQTL ® 5, Software for the mapping of quantitative trait loci in experimental populations. Kyazma B.V., Wageningen, Netherlands.
- Van Ooijen, 2006. JoinMap ® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., Wageningen, Netherlands.
- Van Ooijen & Jansen (eds), 1994. Biometrics in Plant Breeding: Applications of Molecular Markers. Proc. 9th Meeting Eucarpia Section Biometrics. Plant Research International, Wageningen, 272 pp.
- Van Ooijen & Maliepaard, 1996. MapQTL version 3.0: Software for the calculation of QTL positions on genetic maps. Plant Genome IV Abstracts.
- Zeng, 1994. Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
If needed, support will be given to help you get the software running and solve problems not described in the manual. This support is limited to advice by e-mail to <support(at)kyazma.nl>. A list of frequently asked questions is presented at this web site.