Report on Quantitative Trait Loci (QTL) Mapping Software
for Crosses Between Inbred Lines
February 1997
by Steve J. Knapp
[ed. by Brian S. Yandell]

A workshop was held in February, 1997, on Quantitative Genetics and Biotechnology to survey participants on the attributes of several software packages for mapping QTL and to define the analytical needs which are not presently met by software packages. The workshop covered software for mapping QTL in inbred and outbred populations. Only the former are covered in this report.

World Wide Web links to many, if not most, of the QTL mapping software packages can be found at a website created by Brian S. Yandell (Departments of Statistics and Horticulture, University of Wisconsin-Madison): Developers and users may wish to alert Brian ( to packages which are not listed at the website. Other websites that maintain genetic software lists include the following:

The packages discussed at the workshop were:

Two additional packages were mentioned:

A concensus was reached that there is considerable overlap in the kinds of matings handled and statistics produced by the various QTL mapping software packages. Some packages are more sophisticated in their handling of genome search and multilocus QTL parameter estimation.

The software research and development needs identified by workshop participants are detailed below. Comments specific to certain packages or from software developers are indented. Further comments are most welcome.

  1. Multilocus Interval Mapping. Several packages use interval mapping methods, but none have built in functions for multilocus interval mapping (simultaneous search of more than one chromosome segment).
  2. Discrete Traits. Although methods have been described for mapping discrete or ordinal traits, e.g., threshold traits and disease resistance traits with arbitrary scales, none of the packages explicitly handles such traits.
  3. Dominant Markers. When populations are segregating for dominant and codominant markers, interval mapping functions are needed for dominant x dominant, dominant x codominant, and codominant x codominant marker brackets.
  4. Multivariate Analyses. Multivariate QTL mapping methods are needed to estimate QTL genetic correlations and correlated QTL effects and for estimating marker-assisted selection index parameters for multiple traits.
  5. Random and Mixed Effects Models. QTL or marker effects are often handled as fixed effects in QTL mapping experiments. There are circumstances where they might be handled as random effects, e.g., QTL or marker variance component estimates are needed for implementing marker-assisted index selection. There is merit to developing software for handling QTL or marker effects as random effects. Random effects interval mapping methods have been described, but have not yet been implemented in any QTL mapping software packages. QTL mapping software does not presently handle a full gamut of mixed linear model problems, e.g., experiment and environment designs, random polygenic variances,
  6. Marker-Assisted Selection Index Parameters. Software has not been developed for directly estimating marker-assisted index selection parameters (marker and genetic variances and marker index weights and scores). Estimates of these parameters must be patched together from the output of QTL mapping software or widely used statistical analysis packages (e.g., SAS). Some of the technical details for estimating MAS index parameters are not trivial and have not been worked out, e.g., selecting for two or more traits or across two or more generations. The ultimate package would permit the user to handle a wide variety of random and mixed effects estimation and selection index problems.
  7. Backcross Inbred Matings. Most of the packages surveyed handle backcross, doubled haploid, recombinant inbred, and F2, F3, ..., Ft progeny. None explicitly handle advanced backcross generations (BC2, BC3, ..., BCt) or inbred lines developed from backcross or advanced backcross generations (other than BC1S1).
Thanks to coordinating efforts of Bill Beavis, Pioneer Seed, IA, and comments from the following software developers:
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Last modified: Wed Jul 16 16:38:02 1997 by Brian Yandell (