Phylogenetics of rat inbred strains

Thomas, Michael A.; Chen, Chin-Fu; Jensen‐Seaman, Michael I.; Tonellato, Peter J.; Twigger, Simon

doi:10.1007/s00335-002-2204-5

Cited by 42 publications

(39 citation statements)

References 30 publications

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“…Previous analysis on microsatellites suggested that Brown Norway (BN) was genetically most similar to wild rats and furthest away from laboratory rat strains (Canzian 1997;Thomas et al 2003). Although the current genotyping data is not sufficient to build a reliable phylogenetic tree, our results confirm that Brown Norway is clearly most distant from the other inbred strains tested.…”

Section: Snps Between Inbred Strainssupporting

confidence: 59%

“…In rat strain databases, the DA strain is suggested to be closely related to the COP strain (http:// rgd.mcw.edu/strains/; http://www.mh-hannover.de/institute/ tierlabor/da.html), but in our set DA and COP share only 85% of the alleles. Of course, many more polymorphic loci should be explored to reliably trace the history of rat inbred strains, as illustrated by the results of Canzian (1997) and Thomas et al (2003), showing close relationship between DA and COP using 995 and 4800 microsatellite markers, respectively.…”

Section: Snps Between Inbred Strainsmentioning

confidence: 99%

“…Currently, information on genetic variation in rat laboratory strains is limited to a set of microsatellite markers (Canzian 1997;Thomas et al 2003) that are generally located in noncoding regions. In this study, we focused on single nucleotide polymorphisms (SNPs) in gene coding regions of rat inbred strains.…”

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confidence: 99%

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Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains

Smits¹,

Zutphen²,

Plasterk³

et al. 2004

Genome Res.

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Single nucleotide polymorphisms (SNPs) are the most common genetic variation in mammalian populations. Their significance is illustrated by their potential contribution to common disease but also by their potential for use in genetic association and mapping experiments. We have examined the genetic variation between commonly used inbred rat strains by using an efficient SNP discovery and typing assay based on enzyme-based (CEL I) heteroduplex cleavage. Screening of a panel of 96 different rat (sub-)strains for 100 genomic loci in 55 genes, whose human homologs are implicated in clinically relevant diseases like neurological disorder, cancer, schizophrenia, and obesity, resulted in the identification of 103 novel polymorphisms. As all strains are simultaneously genotyped in this setup, this allowed us to make an estimate of the genetic variation between and within commonly used rat inbred strains. Interestingly, we observed substantial genetic variation between colonies of the same inbred strain, maintained at different locations. Furthermore, we identified 17 non-synonymous SNPs that may have an effect on protein function and contribute to phenotypic differences between different laboratory strains.

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Section: Snps Between Inbred Strainssupporting

confidence: 59%

Section: Snps Between Inbred Strainsmentioning

confidence: 99%

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Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains

Smits¹,

Zutphen²,

Plasterk³

et al. 2004

Genome Res.

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“…The progenitor strains for breeding the rat test population were selected based on the following criteria: (1) past use of the strains in anthrax-related studies, 1,2 (2) maximal diversity in the host background determined from the Strain Calculator, (3) estimated separation on the phylogenetic tree 21,22 and (4) commercial availability of the strains. Breeding pairs of inbred F344 (F344/DuCRL ordered as CDF), WKY (WKY/NCrl), LEW (LEW/Crl) and BN (BN/Mcwi) rats were purchased from Charles River Laboratories (CRL, Wilmington, MA, USA).…”

Section: Generation Of the Rat Test Populationmentioning

confidence: 99%

Rat survival to anthrax lethal toxin is likely controlled by a single gene

et al. 2007

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We examined whether survival of different rat strains administered anthrax lethal toxin is genetically determined. A reproducible test population of first filial generation hybrid rats was bred based on the susceptibility of progenitors to anthrax lethal toxin and to maximize genetic diversity across the strains. These rats were then tested with varying doses of anthrax lethal toxin. We found that all 'sensitive' strains died within 2 h following systemic administration of 240 mg/kg lethal toxin, while one strain survived following a five times higher dose (1.4 mg/kg). The ability of lethal toxin to lyse macrophage cultures derived from the bone marrow of these strains corresponded with in vivo results. We conclude that a rat test population can detect strain differences in response to anthrax lethal toxin. Survival is influenced by the host genome background and is likely due to a single gene with a recessive mode of inheritance.

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“…In addition, since the Brown Norway (BN) inbred rat strain is genetically closer to wild rats than it is to other inbred rat strains, the predicted sequence may not be identical to the Nat3 ORF found in other common inbred rat strains (Canzian, 1997;Thomas et al, 2003). The aims of this study included complete sequencing of the putative rat Nat3 gene from three inbred rat strains, cloning the putative rat Nat3 ORF into a prokaryotic expression vector, and recombinant expression of the rat Nat3 gene in a high expressing bacterial system to characterize Nat3 catalytic activity, substrate selectivity, and intrinsic stability.…”

mentioning

confidence: 99%

Identification and Characterization of Functional Rat Arylamine N-Acetyltransferase 3: Comparisons with Rat Arylamine N-Acetyltransferases 1 and 2

Walraven¹,

Doll²,

Hein³

2006

J Pharmacol Exp Ther

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Arylamine N-acetyltransferases (NATs; EC 2.3.1.5) catalyze both the N-acetylation and O-acetylation of arylamines and Nhydroxyarylamines. Humans possess two functional N-acetyltransferase genes, NAT1 and NAT2, as well as a nonfunctional pseudogene, NATP. Previous studies have identified Nat1 and Nat2 genes in the rat. In this study, we identified and characterized a third rat N-acetyltransferase gene (Nat3) consisting of a single open reading frame of 870 base pairs encoding a 290-amino acid protein, analogous to the previously identified human and rat N-acetyltransferase genes. Rat Nat3 nucleotide sequence was 77.2 and 75.9% identical to human NAT1 and NAT2, respectively. Rat Nat3 amino acid sequence was 68.6 and 67.2% identical to human NAT1 and NAT2, respectively. Rat Nat1, Nat2, and Nat3 were each cloned and recombinantly expressed in Escherichia coli. Recombinant rat Nat3 exhibited thermostability intermediate between recombinant rat Nat1 and Nat2. Recombinant rat Nat3 was functional and catalyzed the N-acetylation of several arylamine substrates, including 3-ethylaniline, 3,5-dimethylaniline, 5-aminosalicylic acid, 4-aminobiphenyl, 4,4Ј-methylenedianiline, 4,4Ј-methylenebis(2-chloroaniline), and 2-aminofluorene, and the O-acetylation of N-hydroxy-4-aminobiphenyl. The relative affinities of arylamine carcinogens such as 4-aminobiphenyl, N-hydroxy-4-aminobiphenyl, and 2-aminofluorene for N-and O-acetylation via recombinant rat Nat3 were comparable with recombinant rat Nat1 and higher than for recombinant rat Nat2. This study is the first to report a third arylamine N-acetyltransferase isozyme with significant functional capacity.

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Phylogenetics of rat inbred strains

Cited by 42 publications

References 30 publications

Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains

Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains

Rat survival to anthrax lethal toxin is likely controlled by a single gene

Identification and Characterization of Functional Rat Arylamine N-Acetyltransferase 3: Comparisons with Rat Arylamine N-Acetyltransferases 1 and 2

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