Genetic Maps of the Rat Genome

Release Seven (Final), January 2000

Genetic Maps of the Rat

These pictures represent genetic linkage maps of the rat resulting from the integration of two F2 intercrosses (SHRSP x BN and FHH x ACI). There are a total of 4,786 markers on these maps; 4375 WIBR/MIT CGR markers; 223 markers from the previously released Mit/Mgh rat maps and 188 markers from the National Institute of Arthritis and Musculoskeletal and Skin Diseases "Arb" rat maps. View a table listing number of markers by cross, type and chromosome or download the table via anonymous ftp.

Map Description

The left hand side of each picture represents the SHRSP x BN cross and the right hand side the FHH x ACI cross. Markers in common between the two crosses are connected by a line to define integration points. Pictures are drawn to a scale of 5cm (Kosombi) per inch. The changes in color of the backbone of the chromosome for each cross represents the space between any two framework loci. Markers in blue type are framework loci. Markers in green type are unique placement loci. Markers in black type are "bouncy" placement loci.

You will find that map distances between markers will vary from cross to cross but order should be well preserved. We welcome observations of potentially erroneous marker placements. Please report these to: Robert Steen: Please include the type of cross you used (F2 intercross, backcross, etc.), the strains used in the cross, the number of animals genotyped, the method of genotyping (EtBR agarose, P32-PAGE, ABI377-fluorescence, etc) and the observations you made.

Browse the Integrated Genetic Maps WIBR/MIT CGR Version 7

Note: Chromosome orientations utilized were as determined in the following publication: Spirer, et. al. (1998). Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution. Mammalian Genome 9, 721-734.

If you desire hard copies of these images, they are available via anonymous ftp in three formats: PDF , PICT and POSTSCRIPT . These files have been scaled to fit on a standard 8.5 X 11 inch page and therefore each image has a distinct hash scale at the bottom in Kosambi centiMorgans. The original files (scaled 5 Kosambi cM per inch are also available as PICTs and GIFs.

  • Chr1
  • Chr2
  • Chr3
  • Chr4
  • Chr5
  • Chr6
  • Chr7
  • Chr8
  • Chr9
  • Chr10
  • Chr11
  • Chr12
  • Chr13
  • Chr14
  • Chr15
  • Chr16
  • Chr17
  • Chr18
  • Chr19
  • Chr20
  • ChrX

  • About Old Releases

    Old releases of the WIBR/MIT CGR maps are no longer available via our web server in html format with the exception of the original MIT/MGH maps (Release One) and the maps and data published in Mammalian Genome (1998). The maps and data of all the old releases are available by anonymous ftp as zipped archives (filename.tar.gz).

    Data from Mammalian Genome, 9:521-530 (1998)

    Browse the Integrated Genetic Maps Data

    Genotype Data for Integrated Maps (gene-names)

    Genotype Data for Integrated Maps (locus names)

    Primer Sequence for Integrated Maps

    Allele Size Data for Integrated Maps

    Downloand the Integrated Genetic Maps Data

    Download Data for Integrated Genetic Maps via anonymous ftp

    Download pdf files of the Integrated Genetic Maps via anonymous ftp

    Browse the Integrated Genetic Maps

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    Database Searches for Polymorphism and Primer Sequence Information

    We offer a direct query interface to our database so that you may obtain polymorphism and sequence information about most markers in this release. For more detailed information about inbred rat strains visit the Jackson Laboratories web site.

    Search for markers by position/polymorphism

    View polymorphism table for all markers or download the polymorphism table via anonymous ftp. Note: Polymorphism data is calculated only for loci that amplified successfully in any given strain. To view statistics for these calculations you may view the following table--polymorphism information with marker numbers. Warning--This is a very large table! In each square the number to the left represents the percent polymorphism, the top number on the right is the number of monomorphic markers, the middle is the number of polymorphic markers and the bottom is the number of null markers (null meaning a score of -1 which means failure of that strain to amplify). For example: If you look at the strains AVN versus ACI, there were a total of 4,733 markers analyzed of which 1641 were mono, 2123 were poly and 969 were null (-1). Thus the two strains exhibit a polymorphism rate of 56%--(2123 / (2123 + 1641)).

    Search for marker information by marker's name

    Please note that the data representing the four strains used for the two mapping crosses was generated here at the WIBR/MIT CGR in a seperate experiment from the remaining 48 strains which were characterized at the Medical College of Wisconsin. Therefore, you may find that artificial polymorphisms result if you use too small a base pair tolerance when comparing one of these four strains to strains in the 48 strain group. However, within either the four strain group or the 48 strain group you may choose a tolerance of as small as you like and it should yield accurate polymorphism data.  When using the above cgi-search you will not encounter this problem as each strain is represented by the MCW data with the exceptions of SHR/MIT and BN/MIT.

    For more information regarding allele sizes please contact Jo Gullings-Handley of the Jacob Lab at the Medical College of Wisconsin.

    Primer sequences, original clone sequences, genetic positions and genotypes for all DNRatN and most other rat sslp's are available in various flat files by anonymous ftp.

    Primer data is available in a single flat file (markers.txt) containing the lab assay name, locus name, forward and reverse primer sequences and predicted product size based on original clone sequence.

    Original clone sequences for most markers are available in 42 separate files (ChrN_cross.txt) (top = SHRSP x BN; bottom = FHH x ACI) each containing the marker's locus name and clone sequence from which it was derived.

    The genetic position data for each marker is available in 42 separate files (top = SHRSP x BN; bottom = FHH x ACI) containing locus name, lab assay name, placement type, and genetic distance in Kosambi centimorgans.

    Genotype data for each marker is available in 42 separate files (ChrN_cross.txt) (top = SHRSP x BN; bottom = FHH x ACI) each containing the marker's locus names and genotypes for that particular cross and chromosome.

    For more information regarding any of this data please contact Robert Steen.

    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.

    Rat YAC Library Information

    In addition to our work on the rat genetic map, we have developed a YAC library which has been 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 has made this resource available to the research community. Please see the Research Genetics online catalog for details. You may also address inquiries regarding pricing and availability of this resource to (

    The manuscript describing the rat YAC library is the following:

    M.L. Haldi, P. Lim, K. Kaphingst, U. Akella, J. Whang, and E.S. Lander (1997). Construction of a large-insert yeast artifical chromosome library of the rat genome. Mammalian Genome 8, 284.

    In addition, the methods followed were extremely similiar to those used in the construction of the mouse YAC library. These methods are described in the following publication:

    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.

    Citing The Whithead/MIT CGR Map Data

    Citation: The information in this data release should be referenced in publications as:

    Markers from Release Six and earlier may be referenced using the May, 1999 Genome Research article by Steen, R.G. et al.

    Markers appearing in this final release, not previously reported, may be referenced as: Whitehead Institute/MIT Center for Genome Research, Rat Genomic Mapping Project, Data Release 7 (January, 2000), Steen, R.G. et al.

    For further information contact:

    Informatics Questions

    Bill VanEtten

    Scientific Questions

    Robert Steen:

    Whitehead Institute/MIT Center for Genome Research