Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidatesReport as inadecuate




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BMC Genomics

, 6:170

First Online: 29 November 2005Received: 23 September 2005Accepted: 29 November 2005

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.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-6-170 contains supplementary material, which is available to authorized users.

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Author: Bart MG Smits - Victor Guryev - Dimphy Zeegers - Dirk Wedekind - Hans J Hedrich - Edwin Cuppen

Source: https://link.springer.com/article/10.1186/1471-2164-6-170







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