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SNP and haplotype mapping for genetic analysis in the rat
1Max-Delbrück Center for Molecular Medicine, Robert-Rossle-Strae 10, 13125 Berlin, Germany.
Nature Genetics
|April 30, 2008
Summary
Researchers mapped genetic variations in laboratory rats using millions of single nucleotide polymorphisms (SNPs). This detailed SNP map enhances disease gene discovery and physiological studies in this key model organism.
Area of Science:
- Genetics
- Animal Models
- Genomics
Background:
- The laboratory rat (Rattus norvegicus) is a crucial model organism in biomedical research.
- Inbred rat strains, derived from limited founder populations, offer valuable genetic variation for genotype-phenotype correlation.
- Existing genetic tools require augmentation for comprehensive physiological studies.
Purpose of the Study:
- To survey genetic variation in laboratory rat strains using single nucleotide polymorphisms (SNPs).
- To construct high-density genetic maps for improved disease gene mapping.
- To provide a community resource of characterized SNPs and genetic maps.
Main Methods:
- Identification and genotyping of nearly 3 million novel SNPs.
- Accurate genotyping of 20,238 SNPs across 167 inbred rat strains, two recombinant inbred panels, and an F2 intercross.
- Construction of high-density genetic maps utilizing 81% of the characterized SNPs.
Main Results:
- A comprehensive dataset of 20,238 characterized SNPs was generated.
- High-density genetic maps were constructed, aiding in disease gene mapping.
- Population structure and linkage disequilibrium patterns were elucidated.
- The utility of the SNP map for quantitative trait loci (QTL) mapping was demonstrated.
Conclusions:
- The study provides a valuable, openly available SNP map resource for the research community.
- This resource significantly enhances the genetic toolkit for laboratory rat research.
- The findings facilitate genotype-phenotype correlations and disease gene discovery in this model organism.
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01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...