RGD Reference Report - SNP and haplotype mapping for genetic analysis in the rat. - Rat Genome Database

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SNP and haplotype mapping for genetic analysis in the rat.

Authors: Saar, K  Beck, A  Bihoreau, MT  Birney, E  Brocklebank, D  Chen, Y  Cuppen, E  Demonchy, S  Dopazo, J  Flicek, P  Foglio, M  Fujiyama, A  Gut, IG  Gauguier, D  Guigo, R  Guryev, V  Heinig, M  Hummel, O  Jahn, N  Klages, S  Kren, V  Kube, M  Kuhl, H  Kuramoto, T  Kuroki, Y  Lechner, D  Lee, YA  Lopez-Bigas, N  Lathrop, GM  Mashimo, T  Medina, I  Mott, R  Patone, G  Perrier-Cornet, JA  Platzer, M  Pravenec, M  Reinhardt, R  Sakaki, Y  Schilhabel, M  Schulz, H  Serikawa, T  Shikhagaie, M  Tatsumoto, S  Taudien, S  Toyoda, A  Voigt, B  Zelenika, D  Zimdahl, H  Hubner, N  Hubner, Norbert 
Citation: Saar K, etal., Nat Genet. 2008 May;40(5):560-6.
RGD ID: 2292911
Pubmed: PMID:18443594   (View Abstract at PubMed)
PMCID: PMC5915293   (View Article at PubMed Central)
DOI: DOI:10.1038/ng.124   (Journal Full-text)

The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.



Objects referenced in this article
Strain ACI/Eur August x Copenhagen Irish Rattus norvegicus
Strain ACI/N A X C 9935, Irish Rattus norvegicus
Strain ACI/NKyo august copenhagen irish Rattus norvegicus
Strain ACI/NSlc null Rattus norvegicus
Strain ACI/SegHsd null Rattus norvegicus
Strain ACI/Ztm null Rattus norvegicus
Strain ACI/ZtmKini null Rattus norvegicus
Strain AUG/OlaHsd null Rattus norvegicus
Strain BB/OK BioBreeding rat Rattus norvegicus
Strain BB/WorTky BioBreeding rat Rattus norvegicus
Strain BDE/Ztm null Rattus norvegicus
Strain BDII/Ztm null Rattus norvegicus
Strain BDIV/lfz null Rattus norvegicus
Strain BDIX/Han null Rattus norvegicus
Strain BDIX/Ifz null Rattus norvegicus
Strain BDV/Ztm null Rattus norvegicus
Strain BH/Ztm null Rattus norvegicus
Strain BN-Lx/Cub Brown Norway with polydactyly-luxate Rattus norvegicus
Strain BN/Crl null Rattus norvegicus
Strain BN/HanKini null Rattus norvegicus
Strain BN/NHsdMcwi null Rattus norvegicus
Strain BN/Rj null Rattus norvegicus
Strain BN/SsNHsd null Rattus norvegicus
Strain BN/SsNSlc null Rattus norvegicus
Strain BN/Ztm null Rattus norvegicus
Strain BS/Ztm null Rattus norvegicus
Strain BUF/Mna null Rattus norvegicus
Strain BUF/SimRijHsd null Rattus norvegicus
Strain BXH10/Cub null Rattus norvegicus
Strain BXH11/Cub null Rattus norvegicus
Strain BXH12/Cub null Rattus norvegicus
Strain BXH13/Cub null Rattus norvegicus
Strain BXH2/Cub null Rattus norvegicus
Strain BXH3/Cub null Rattus norvegicus
Strain BXH5/Cub null Rattus norvegicus
Strain BXH6/Cub null Rattus norvegicus
Strain BXH8/Cub null Rattus norvegicus
Strain BXH9/Cub null Rattus norvegicus
Strain CDR/Ygl null Rattus norvegicus
Strain CDS/Ygl Cohen diabetic-sensitive rat Rattus norvegicus
Strain COP/CrCrl null Rattus norvegicus
Strain COP/OlaHsd null Rattus norvegicus
Strain DA.BI.RT1i-(D20Rat42-D20Rat31)/Rhd null Rattus norvegicus
Strain DA.LEW.RT1f-(D20Wox15-D20Wox13)/Rhd null Rattus norvegicus
Strain DA/OlaHsd null Rattus norvegicus
Strain DA/Slc dark agouti Rattus norvegicus
Strain DA/ZtmKini null Rattus norvegicus
Strain DMY/Kyo demyelination rat Rattus norvegicus
Strain DON/Kyo Donryu rat Rattus norvegicus
Strain DRH/Seac null Rattus norvegicus
Strain E3/Ztm null Rattus norvegicus
Strain E3/ZtmRhd null Rattus norvegicus
Strain F344/NCrl null Rattus norvegicus
Strain F344/NSlc null Rattus norvegicus
Strain F344/NTac null Rattus norvegicus
Strain F344/Stm null Rattus norvegicus
Strain F344/Ztm null Rattus norvegicus
Strain FHH/EurMcwi null Rattus norvegicus
Strain FHL/EurMcwi Fawn Hooded Low blood pressure Rattus norvegicus
Strain FXLE12/Stm null Rattus norvegicus
Strain FXLE13/Stm null Rattus norvegicus
Strain FXLE14/Stm null Rattus norvegicus
Strain FXLE15/Stm null Rattus norvegicus
Strain FXLE16/Stm null Rattus norvegicus
Strain FXLE17/Stm null Rattus norvegicus
Strain FXLE18/Stm null Rattus norvegicus
Strain FXLE19/Stm null Rattus norvegicus
Strain FXLE20/Stm null Rattus norvegicus
Strain FXLE21/Stm null Rattus norvegicus
Strain FXLE22/Stm null Rattus norvegicus
Strain FXLE23/Stm null Rattus norvegicus
Strain FXLE24/Stm null Rattus norvegicus
Strain FXLE26/Stm null Rattus norvegicus
Strain GAERS/Mave Genetic Absence Epilepsy Rats from Strasbourg Rattus norvegicus
Strain GH/OmrMcwi null Rattus norvegicus
Strain GK/KyoSwe Goto Kakizaki Rattus norvegicus
Strain GK/Slc Goto Kakizaki Rat Rattus norvegicus
Strain HAA/FDSC Hatano High Avoidance Rattus norvegicus
Strain HTX/Kyo hydrocephalus texas Rattus norvegicus
Strain HWY/Slc hairless wistar yagi Rattus norvegicus
Strain HXB1/Ipcv null Rattus norvegicus
Strain HXB10/Ipcv null Rattus norvegicus
Strain HXB13/Ipcv null Rattus norvegicus
Strain HXB14/Ipcv null Rattus norvegicus
Strain HXB15/Ipcv null Rattus norvegicus
Strain HXB17/Ipcv null Rattus norvegicus
Strain HXB18/Ipcv null Rattus norvegicus
Strain HXB2/Ipcv null Rattus norvegicus
Strain HXB20/Ipcv null Rattus norvegicus
Strain HXB21/Ipcv null Rattus norvegicus
Strain HXB22/Ipcv null Rattus norvegicus
Strain HXB23/Ipcv null Rattus norvegicus
Strain HXB24/Ipcv null Rattus norvegicus
Strain HXB25/Ipcv null Rattus norvegicus
Strain HXB27/Ipcv null Rattus norvegicus
Strain HXB29/Ipcv null Rattus norvegicus
Strain HXB3/Ipcv null Rattus norvegicus
Strain HXB31/Ipcv null Rattus norvegicus
Strain HXB4/Ipcv null Rattus norvegicus
Strain HXB5/Ipcv null Rattus norvegicus
Strain HXB7/Ipcv null Rattus norvegicus
Strain IS/Kyo ishibashi rat Rattus norvegicus
Strain KDP/Tky Komeda diabetes-prone rat Rattus norvegicus
Strain KHR/Kyo kaken hairless rat Rattus norvegicus
Strain KND/Tky komeda non-diabetic rat Rattus norvegicus
Strain LAA/FDSC Hatano Low Avoidance Rattus norvegicus
Strain LE/Stm null Rattus norvegicus
Strain LE/Ztm null Rattus norvegicus
Strain LEA/Hok Long Evans Agouti Rattus norvegicus
Strain LEC/Hok Long Evans Cinnamon Rattus norvegicus
Strain LEJ/Hkm null Rattus norvegicus
Strain LEW.1AV1/Kini null Rattus norvegicus
Strain LEW/Crl Lewis Rattus norvegicus
Strain LEW/Han null Rattus norvegicus
Strain LEW/Jms null Rattus norvegicus
Strain LEW/NHsd null Rattus norvegicus
Strain LEW/SsNSlc null Rattus norvegicus
Strain LEXF10A/Stm null Rattus norvegicus
Strain LEXF10B/Stm null Rattus norvegicus
Strain LEXF10C/Stm null Rattus norvegicus
Strain LEXF11/Stm null Rattus norvegicus
Strain LEXF1A/Stm null Rattus norvegicus
Strain LEXF1C/Stm null Rattus norvegicus
Strain LEXF2A/Stm null Rattus norvegicus
Strain LEXF2B/Stm null Rattus norvegicus
Strain LEXF2C/Stm null Rattus norvegicus
Strain LEXF3/Stm null Rattus norvegicus
Strain LEXF4/Stm null Rattus norvegicus
Strain LEXF5/Stm null Rattus norvegicus
Strain LEXF6B/Stm null Rattus norvegicus
Strain LEXF7A/Stm null Rattus norvegicus
Strain LEXF7B/Stm null Rattus norvegicus
Strain LEXF7C/Stm null Rattus norvegicus
Strain LEXF8A/Stm null Rattus norvegicus
Strain LEXF8D/Stm null Rattus norvegicus
Strain LEXF9/Stm null Rattus norvegicus
Strain LH/Mav null Rattus norvegicus
Strain LN/Mav null Rattus norvegicus
Strain LOU/CHan Louvain Rattus norvegicus
Strain LOU/Ins null Rattus norvegicus
Strain LUDW/OlaHsd Ludwig Rattus norvegicus
Strain MES/Slc Matsumoto Eosinophilia Shinshu Rattus norvegicus
Strain MHS Milan Hypertensive Strain Rattus norvegicus
Strain MNS Milan normotensive strain Rattus norvegicus
Strain MNS/Gib Milan Normotensive Strain Rattus norvegicus
Strain MWF/Hsd Munich Wistar Fromter Rattus norvegicus
Strain NAR/SaU non-albumin rat Rattus norvegicus
Strain NE/Mave null Rattus norvegicus
Strain NER/Kyo Noda epileptic rat, GMS Rattus norvegicus
Strain OM/NSlc Osborne-Mendel rat Rattus norvegicus
Strain OM/Ztm Osborne-Mendel Rattus norvegicus
Strain PAR/Wsl null Rattus norvegicus
Strain PVG.1AV1/Kini null Rattus norvegicus
Strain PVG/Seac Piebald Virol Glaxo Rattus norvegicus
Strain PXO1/Cub null Rattus norvegicus
Strain PXO10/Cub null Rattus norvegicus
Strain PXO2/Cub null Rattus norvegicus
Strain PXO3-1/Cub null Rattus norvegicus
Strain PXO3-2/Cub null Rattus norvegicus
Strain PXO4/Cub null Rattus norvegicus
Strain PXO5-1/Cub null Rattus norvegicus
Strain PXO5-2/Cub null Rattus norvegicus
Strain PXO6-1/Cub null Rattus norvegicus
Strain PXO6-2/Cub null Rattus norvegicus
Strain PXO6-3/Cub null Rattus norvegicus
Strain PXO7-1/Cub null Rattus norvegicus
Strain PXO7-2/Cub null Rattus norvegicus
Strain PXO8-1/Cub null Rattus norvegicus
Strain PXO8-2/Cub null Rattus norvegicus
Strain PXO9/Cub null Rattus norvegicus
Strain RCS/Kyo royal college of surgeons rat Rattus norvegicus
Strain RICO/Ngs null Rattus norvegicus
Strain SBH/Ygl Sabra hypertension prone Rattus norvegicus
Strain SBN/Ygl Sabra hypertension resistant Rattus norvegicus
Strain SER/Kyo spontaneously epileptic rat Rattus norvegicus
Strain SHHF/Bbb null Rattus norvegicus
Strain SHR.BN-(D18Rat32-D18Rat12)/Ipcv null Rattus norvegicus
Strain SHR.BN-(D8Mit5-D8Mgh6)/Ipcv null Rattus norvegicus
Strain SHR.BN10/Ipcv null Rattus norvegicus
Strain SHR/1NCrl null Rattus norvegicus
Strain SHR/Izm null Rattus norvegicus
Strain SHR/Kyo spontaneous hypertension rat Rattus norvegicus
Strain SHR/Mol null Rattus norvegicus
Strain SHR/NCrl null Rattus norvegicus
Strain SHR/NHsd null Rattus norvegicus
Strain SHR/OlaIpcv null Rattus norvegicus
Strain SHRSP Spontaneously Hypertensive Rat, Stroke Prone Rattus norvegicus
Strain SHRSP.SHRSR-(D1Rat134-Mt1-ps1)/Bbb null Rattus norvegicus
Strain SHRSP.SHRSR-(Klk1-D1Mit3)/Bbb null Rattus norvegicus
Strain SHRSP.SHRSR-(Klk1-Mt1-ps1)/Bbb null Rattus norvegicus
Strain SHRSP.WKY-(D2Mit21-D2Rat157)/Gcrc null Rattus norvegicus
Strain SHRSP.WKY-(D2Mit5-D2Rat133)/Gcrc null Rattus norvegicus
Strain SHRSP.WKY-(D2Rat13-D2Rat157)/Gcrc null Rattus norvegicus
Strain SHRSP.WKY-(D2Rat132-D2Rat53)/Gcrc null Rattus norvegicus
Strain SHRSP.WKY-(D2Wox15-D2Rat133)/Gcrc null Rattus norvegicus
Strain SHRSP.WKY-(D2Wox9-D2Mgh12)/Gcrc null Rattus norvegicus
Strain SHRSP/Ezo null Rattus norvegicus
Strain SHRSP/Gcrc Spontaneously hypertensive rat, stroke prone Rattus norvegicus
Strain SHRSP/Izm null Rattus norvegicus
Strain SHRSP/Ngsk null Rattus norvegicus
Strain SHRSR.SHRSP-(D1Rat134-Mt1-ps1)/Bbb null Rattus norvegicus
Strain SHRSR.SHRSP-(Klk1-Mt1-ps1)/Bbb null Rattus norvegicus
Strain SPRD/Ztm null Rattus norvegicus
Strain SR/JrHsd Dahl Salt-Resistant Rattus norvegicus
Strain SS/Jr Salt Sensitive Rattus norvegicus
Strain SS/JrHsd Dahl Salt-Sensitive Rattus norvegicus
Strain SS/JrHsdMcwi null Rattus norvegicus
Strain T2DN/Mcwi null Rattus norvegicus
Strain THE/Utp Tsukuba high-emotional rat Rattus norvegicus
Strain TLE/Utp Tsukuba low-emotional rat Rattus norvegicus
Strain TM/Kyo tester moriyama rat Rattus norvegicus
Strain TO/Hkm null Rattus norvegicus
Strain TRM/Kyo tremor rat Rattus norvegicus
Strain TRMR/Kyo tremor resistant Rattus norvegicus
Strain W/Kyo null Rattus norvegicus
Strain WAG/OlaHsd null Rattus norvegicus
Strain WAG/RijKyo null Rattus norvegicus
Strain WBN/KobSlc wistar bonn/kobori Rattus norvegicus
Strain WF/Kop null Rattus norvegicus
Strain WIAR/Iar Inbred Wistar-Imamichi Rattus norvegicus
Strain Wild1/Hubr null Rattus norvegicus
Strain WKA/Seac null Rattus norvegicus
Strain WKAH/HkmSlc Wistar King A, Hokkaido Rattus norvegicus
Strain WKAH/Hok Wistar-King Aptekman Hokkaido Rattus norvegicus
Strain WKY.SHRSP-(Asgr1-Vamp2)/Bbb null Rattus norvegicus
Strain WKY.SHRSP-(Mt1pa-D1Rat200)/Bbb null Rattus norvegicus
Strain WKY/Bbb null Rattus norvegicus
Strain WKY/Gcrc Wistar-Kyoto Rattus norvegicus
Strain WKY/Izm Wistar-Kyoto Rattus norvegicus
Strain WKY/NCrl null Rattus norvegicus
Strain WKY/NMna null Rattus norvegicus
Strain WKY/Ztm null Rattus norvegicus
Strain WKYO/Kyo null Rattus norvegicus
Strain WN/N Inbred Wistar; W/N Rattus norvegicus
Strain WNA/Nshm null Rattus norvegicus
Strain WOKW/K null Rattus norvegicus
Strain WTC/Kyo null Rattus norvegicus
Strain ZI/Kyo null Rattus norvegicus

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