International Mammalian Genome Society


The 13th International Mouse Genome Conference
October 31-November 3, 1999

Table of Contents * Structure * Bioinformatics * Sequence * Mapping * New Tools * Gene Discovery * Developmental * Mutagenesis * Functional Genomics

B12 Cross-Referencing the T31 Whole Genome Radiation Hybrid Data to the High Quality Recombination Map of the Mouse

Lucy Rowe, Mary Barter, Jurgen Naggert, Janan Eppig. The Jackson Laboratory, Bar Harbor, Maine USA

Whole genome radiation hybrids (RH) are facilitating access to genome maps in many species where traditional recombination mapping has been problematic. Major contributions to the understanding of how RH mapping works and does not work is now coming from the mouse model system. Not only has the mouse the most accessible and detailed recombination-based map among the mammals, but mouse genetics also benefits from a tradition of data sharing and pooling that has led to significant insights. RH mapping is a powerful mapping tool, but there are caveats in both gathering and interpreting RH data.

We have developed a highly detailed recombination-based map in a 188 animal interspecific backcross that has been made available to the community for mapping loci. The complete raw data and maps from this cross are available in a community database from our Web site (http://www.jax.org/resources/documents/cmdata). There are now nearly 5000 loci in this data set, which is still growing. These data provide a detailed map of proven locus order to a maximum resolution of 0.5 to 1 cM.

Two years ago we began to apply similar methods to collating the mouse T31 RH data in a single database. As of July 1999 there were over 3150 loci, mostly microsatellite anchor markers typed by several independent laboratories, included in this comprehensive T31 Database (see http://www.jax.org/resources/documents/cmdata/rhmap/RHIntro.html). We have begun building the framework map of known-order anchor markers between the RH and the backcross panels. Since up to the resolution of the backcrosses we can know what the genetic order should be, we can better evaluate the RH results.

In the process of making this map comparison, we have elucidated several problems inherent in RH mapping, in both data gathering and data interpretation/map building. Most of these difficulties can be attenuated by careful attention to data gathering and interpretation methods. We have applied these lessons to the successful framework mapping of microsatellite anchors for the entire length of mouse Chromosome 18. 65 D18Mit- markers form a continuous linkage along Chromosome 18 (genetic length of 41 cM) with all LODs greater than 6. At intervals roughly equivalent to the LOD = 6 these markers are also placed on The Jackson Laboratory interspecific backcrosses, and the order of the markers on the two panels is in complete agreement. We are continuing this work to cross-reference the RH data to the Jackson Backcross data for other chromosomes, to continue to improve the power of RH mapping.

In conclusion, RH mapping appears to be a useful tool for mapping the genomes of disparate species, and the work in the mouse T31 panel points to suggested strategies for obtaining and interpreting RH data for optimum value from this technology.

 


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