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: (View Article at PubMed) PMID:18443594
DOI: Full-text: DOI:10.1038/ng.124

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.

Annotation

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

Additional Information