ArticleBMC genomics2005
Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates.
Article in BMC genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 22 citations in OpenAlex.
- Hematological and biochemical characterization of aging farm male rat strains in the national center for geriatrics and gerontology.Experimental animals · 2025Article
- Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat.G3 (Bethesda, Md.) · 2016Article
- Genomic landscape of rat strain and substrain variation.BMC genomics · 2015Article
- Genes unlinked to the leptin receptor influence urinary albumin excretion in obese Zucker rats.Physiological genomics · 2010Article
- SNP and haplotype mapping for genetic analysis in the rat.Nature genetics · 2008Article
- A genome-wide SNP panel for mapping and association studies in the rat.BMC genomics · 2008Article
- Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers.BMC genomics · 2007Article
- A target-selected Apc-mutant rat kindred enhances the modeling of familial human colon cancer.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Haplotype block structure is conserved across mammals.PLoS genetics · 2006Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe laboratory rat (Rattus norvegicus) is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particularly pharmacogenetic point of view and useful for marker selection for genetic cloning and association studies.
resultsWe show that Single Nucleotide Polymorphisms (SNPs) in commonly used rat strains are surprisingly well represented in wild rat isolates. Shotgun sequencing of 814 Kbp in one wild rat resulted in the identification of 485 SNPs as compared with the Brown Norway genome sequence. Genotyping 36 commonly used inbred rat strains showed that 84% of these alleles are also polymorphic in a representative set of laboratory rat strains.
conclusionWe postulate that shotgun sequencing in a wild rat sample and subsequent genotyping in multiple laboratory or domesticated strains rather than direct shotgun sequencing of multiple strains, could be the most efficient SNP discovery approach. For the rat, laboratory strains still harbor a large portion of the haplotypes present in wild isolates, suggesting a relatively recent common origin and supporting the idea that rat inbred strains, in contrast to mouse inbred strains, originate from a single species, R. norvegicus.
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