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A new method for identifying informative genetic markers in selectively bred rats

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Abstract

Microsatellite length polymorphisms are useful for the mapping of heritable traits in rats. Over 4000 such microsatellites have been characterized for 48 inbred rat strains and used successfully to map phenotypes that differ between strains. At present, however, it is difficult to use this microsatellite database for mapping phenotypes in selectively bred rats of unknown genotype derived from outbred populations because it is not immediately obvious which markers might differ between strains and be informative. We predicted that markers represented by many alleles among the known inbred rat strains would also be most likely to differ between selectively bred strains derived from outbred populations. Here we describe the development and successful application of a new genotyping tool (HUMMER) that assigns “heterozygosity” (Het) and “uncertainty” (Unc) scores to each microsatellite marker that corresponds to its degree of heterozygosity among the 48 genotyped inbred strains. We tested the efficiency of HUMMER on two rat strains that were selectively bred from an outbred Sprague-Dawley stock for either high or low activity in the forced swim test (SwHi rats and SwLo rats, respectively). We found that the markers with high Het and Unc scores allowed the efficient selection of markers that differed between SwHi and SwLo rats, while markers with low Het and Unc scores typically identified markers that did not differ between strains. Thus, picking markers based on Het and Unc scores is a valuable method for identifying informative microsatellite markers in selectively bred rodent strains derived from outbred populations.

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Acknowledgments

We thank Mike Epstein for assistance with statistical analysis and Dan Weinshenker for coining the “HUMMER” acronym. This work was supported in part by the National Heart, Lung, and Blood Institute (#HL64541).

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Authors and Affiliations

  1. Department of Human Genetics, Emory University, Whitehead 301, 615 Michael Street, Atlanta, Georgia, 30322, USA

    David Weinshenker, Malania M. Wilson & Neil E. Lamb

  2. Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, Georgia, 30322, USA

    Katherine M. Williams & Jay M. Weiss

  3. Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA

    Simon N. Twigger

Authors
  1. David Weinshenker
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  2. Malania M. Wilson
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  3. Katherine M. Williams
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  4. Jay M. Weiss
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  5. Neil E. Lamb
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  6. Simon N. Twigger
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Correspondence to David Weinshenker.

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Weinshenker, D., Wilson, M.M., Williams, K.M. et al. A new method for identifying informative genetic markers in selectively bred rats. Mamm Genome 16, 784–791 (2005). https://doi.org/10.1007/s00335-005-0047-6

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  • DOI: https://doi.org/10.1007/s00335-005-0047-6

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