Related Experiment Videos
A new method for identifying informative genetic markers in selectively bred rats
David Weinshenker1, Malania M Wilson, Katherine M Williams
1Department of Human Genetics, Emory University, Whitehead 301, 615 Michael Street, Atlanta, Georgia 30322, USA. dweinshenker@genetics.emory.edu
Summary
A new genotyping tool, HUMMER, efficiently identifies informative microsatellite markers for mapping traits in selectively bred rats. It uses heterozygosity (Het) and uncertainty (Unc) scores to predict marker differences in outbred populations.
Area of Science:
- Genetics and Genomics
- Animal Models
- Bioinformatics
Background:
- Microsatellite length polymorphisms are crucial for mapping heritable traits in rats.
- Existing microsatellite databases are challenging to use for selectively bred rats of unknown genotype.
Purpose of the Study:
- To develop a method for identifying informative microsatellite markers in selectively bred rat strains derived from outbred populations.
- To predict which markers will differ between selectively bred rat strains.
Main Methods:
- Development of a new genotyping tool, HUMMER, assigning heterozygosity (Het) and uncertainty (Unc) scores to microsatellite markers.
- Application of HUMMER to assess microsatellite marker informativeness in Sprague-Dawley derived high and low activity rat strains (SwHi and SwLo).
Main Results:
- Markers with high Het and Unc scores effectively identified differences between SwHi and SwLo rat strains.
- Markers with low Het and Unc scores typically did not differ between the selectively bred strains.
- HUMMER scores accurately predicted marker informativeness for genetic mapping.
Conclusions:
- The HUMMER tool and its Het/Unc scores provide a valuable method for selecting informative microsatellite markers in selectively bred rodent populations.
- This approach enhances the efficiency of genetic mapping in diverse rat models.