Only the former are covered in this report. 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.
Multilocus Interval Mapping. In the implemented part of MQM mapping, markers are used as cofactors to absorb the effects of nearby QTLs, thereby increasing the power for mapping other segregating QTLs. 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. Multi-locus models are not handled this way. 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.