The Comprehensive Mouse Radiation Hybrid Map Densely Cross-Referenced to the Recombination Map: A Tool to Support the Sequence Assemblies

Abstract

We have developed a unique comprehensive mouse radiation hybrid (RH) map of nearly 23,000 markers integrating data from three international genome centers and over 400 independent laboratories. We have cross-referenced this map to the 0.5-cM resolution recombination-based Jackson Laboratory (TJL) backcross panel map, building a complete set of RH framework chromosome maps based on a high density of known-ordered anchor markers. We have systematically typed markers to improve coverage and resolve discrepancies, and have reanalyzed data sets as needed. The cross-linking of the RH and recombination maps has resulted in a highly accurate genome-wide map with consistent marker order. We have compared these linked framework maps to the Ensembl mouse genome sequence assembly, and show that they are a useful medium resolution tool for both validating sequence assembly and elucidating chromosome biology.

Linkage mapping bovine EST-based SNP

“…The genetic map represents the intact living genome, so it is not subject to cloning and assembly problems associated with other mapping and sequencing techniques [17]. However, resolution of the genetic map is limited, and markers that were not separated by recombination in the experimental population cannot be correctly ordered on the linkage map.…”

Molecular characterization, structure and developmental expression of Megane bHLH factor

“…Therefore, Mgn is a single-copy gene in the mouse haploid genome. Despite mouse genome assemblies that are a powerful tool to map genes, some errors have been detected in the mouse sequence assembly (Rowe et al, 2003). Therefore, we used the RH utility to expedite the reliable mapping of the Mgn gene into the mouse genome.…”

Random mutagenesis of proximal mouse chromosome 5 uncovers predominantly embryonic lethal mutations

“…However, in the first step of obtaining a lowresolution map position of a mutation, standard recombination is about as effective. Using the formula of Durrett et al (2002), about 50 F 2 offspring are required to obtain a 10-Mb mapping resolution at 95% confidence using the current value of 2932 Mb comprising the mouse genome and a genetic length of 1355 cM (Rowe et al 2003). Scanning a 50-Mb target region using five deletions of 10 Mb each would use a similar number of mice (∼40; on average, four to rule out a deletion region, plus 24 to implicate a deletion at P < 0.05), but this assumes 100% viability and Mendelian transmission of the deletions, which is often not the case.…”