COMBIN: SOFTWARE FOR ULTRA-DENSE MAPPING

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

ComBin is a software package developed for the construction of ultra-dense genetic maps comprising several thousands of marker loci in offspring of non-inbred parents as well as BC1 and DH populations. The mapping procedure for a cross pollinator data set consists of these steps: 1) Division of the data over three separate sets: - markers segregating in one parent - markers segregating in the other parent - markers heterozygous in both parents 2) Removal of redundancy: All co-segregating markers are grouped in bins. 3) Single-parent maps are built from the bins of the first two data sets: Bins that are separated by a single recombination event are subsequently placed next to each other. This process resembles threading beads on a string. The program allows the formation of branching structures to visualize ambiguities in the data set. After correction of these secondary structures, strings are grouped into linkage groups. 4) The position of markers that are heterozygous in both parents, relative to the first two maps is determined. These allelic bridge 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, as the novel reticulated mapping algorithm immediately visualizes potential scoring errors in the data set.