Genetic Maps of the Rat Genome Release One

Release One, March 1997

What's in this Release?

This is the first formal data release for the Rat Genome Project at the Whitehead Institute/MIT Center for Genome Research. This release of 1,920 genetic markers includes the latest map release from Howard Jacob's Lab at MCW and its integration with mapping data from various other labs (1,001 markers total). In addition, the raw data from the WIBR/MIT mapping effort (919 new markers) is available along with information regarding the Rat YAC library. The WIBR/MIT raw data is currently undergoing error checking as we build new maps. This data is being provided for labs that wish to roughly localize these markers for their use until the new maps are released on this site.

What to Expect in the Next Release...

The next data release will include new maps for the raw data presented in this release as well as the integration of these new maps with the 1,001 marker integrated maps presented in this data release. Allele sizing data, from the 48 strain characterization panel at MCW, for the majority of the markers listed in this release will also be made available. Other possible additions to the next release may include clickable map images to provide detailed access to marker information (original clone sequence, primer sequences, etc.) and polymorphism querying abilities to our database.

Genetic Maps of the Rat

These pictures represent the latest version of the 1,001 marker genetic linkage maps of the rat resulting from the integration of multiple crosses.

The right hand side of each picture (verticle bar with hash marks) is a representation of an integrated map generated from four different crosses (SHR x BN, FHH x ACI, SS/MCW x BN and GH x BN). Markers in bold are the framework markers placed with a LOD confidence of 3.0, markers in italics are placed at a LOD confidence of 2.0 and markers in plain type are placed at a LOD confidence of 1.0. The numbers to the left of the verticle bar represent the relative distances between markers. Map distances are expressed in Centimorgans (cM) and were calculated using Kosambi's map function. There are a total of 645 markers placed on this integrated map.

To the left of the verticle bar are lists of markers from three sources: the GK x BN cross from Dr. Holger Luthman's group at the Karolinska (32 markers), the Oxford Rat Genome Web Page (271 markers) and miscellaneous crosses from Dr. Howard Jacob 's Lab at the Medical College of Wisconsin (53 markers). These markers are placed in a relative position based on markers mapped by each group that are in common with the integrated map (right side of pictures). These markers are not placed with a high degree of confidence, therefore their positions should be taken as a relative "best guess" in relation to the main integrated map. For example, the Oxford maps list three seperate crosses, so we determined orders for these markers based on the reported recombination distances (theta) from each other across all three crosses. These relative orders are being provided to assist investigators looking for markers in specific regions. Since these markers are not placed with a high degree of confidence we would welcome corrections as they become evident from other's data.

Browse the Genetic Maps MGH/MIT Version 2.0

Should you desire hard copies of these images, they are medium resolution gifs and therefore should yield readable images simply by printing them from your web browser (you may need to reduce their size by ~50% to make them fit on a single page).

Map release (Version 1.0 MGH/MIT / January 1995) data

Note: Adjustments and corrections to previous map release (version 1.0 MGH/MIT)

Purchasing Primer Pairs:

All the mapped primers listed in this release are available as MapPairs from Research Genetics, Inc., 2130 Memorial Parkway SW, Huntsville, AL 35801, (800) 533-4363 (phone), (205) 536-9016 (FAX), under a community discount arrangement set up by the Whitehead Institute/MIT Center for Genome Research. (Note: The WIBR/MIT CGR has placed the markers in the public domain. The Center and its personnel receive no financial benefit from the sale of primers.)

Rat YAC Library Information

In addition to our work on the rat genetic map, we have developed a YAC library which is currently being made into DNA pools and spotted onto membranes by Research Genetics, Inc. The library consists of approximately 41,300 clones with an average insert size of 830kb. Genomic DNA from a female of the rat strain, Fisher 344, was inserted into the EcoRI site of the pRML1 and pRML2 vector arms. J57D was used as the yeast host strain. Research Genetics expects to make this resource available to the research community in mid-1997. The release will be announced on their homepage (http://www.resgen.com). Please address inquiries regarding pricing and availability of this resource to (ewick@resgen.com).

A manuscript describing the rat YAC library in detail is currently in preparation. The methods followed were extremely similiar to those used in the construction of the mouse YAC library. These methods are described in the following reference: M.L. Haldi, C. Strickland, P. Lim,V. VanBerkel, X.-N. Chen, D. Noya, J.R. Korenberg, Z. Husain, J. Miller, E.S. Lander (1996). A comprehensive large-insert yeast artificial chromosome library for physical mapping of the mouse genome. Mammalian Genome 7, 767-769.

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All the WIBR/MIT Raw Genotype Data in Flat Files

Note: This is "raw" data and therefore will contain possible errors. As the maps are built the latest error checked data will be provided. Last Updated: 4/4/97

For further information contact:

Informatics Questions (Database and Web Page Contents)

Scientific Questions (Data Production and Background Information)

Robert Steen: steen@genome.wi.mit.edu

Whitehead Institute/MIT Center for Genome Research