CONSTRUCTION OF UTRA-DENSE MAPS USING NOVEL SOFTWARE

Laboratory of Plant Breeding Wageningen University and Research Centre P.O. Box 386 6700 AJ Wageningen The Netherlands

Genetic marker techniques used for genome-wide multi-locus screening like AFLP result in rapidly expanding mapping data sets. Commonly used mapping software is falling short in terms of speed and accuracy. ComBin is a software package developed for the construction of ultra-dense genetic maps comprising several thousands of markers. Novel concepts implemented in ComBin include: 1) Removal of redundancy: All co-segregating markers are placed in bins and subsequent steps are based on ordering bins rather than handling individual markers. 2) Ordering of bins is not based on pair-wise distance. Bins that are separated by a single recombination event are subsequently placed next to each other. 3) By nature, a chromosome is a linear structure, but ComBin allows the formation of branching structures in the initial map. Bins containing markers with scoring errors will not fit in the main axis of the chromosome, which is immediately visualized by the reticulated mapping algorithm. 4) For mapping studies using non-inbred parents (cross pollinators), the maternal and paternal data are handled separately. The positions of bins with 3:1 segregating markers from both parents are determined relative to the parental maps. These positions are plotted in a two-dimensional diagram. ComBin will be a valuable tool in ultra-high density mapping projects, in particular when absolute accuracy is required for future physical mapping studies.