RGD Reference Report - A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains. - Rat Genome Database

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A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains.

Authors: Mashimo, T  Voigt, B  Tsurumi, T  Naoi, K  Nakanishi, S  Yamasaki, K  Kuramoto, T  Serikawa, T 
Citation: Mashimo T, etal., BMC Genet. 2006 Apr 4;7:19.
RGD ID: 1581776
Pubmed: PMID:16584579   (View Abstract at PubMed)
PMCID: PMC1475628   (View Article at PubMed Central)
DOI: DOI:10.1186/1471-2156-7-19   (Journal Full-text)

BACKGROUND: The National Bio Resource Project for the Rat in Japan (NBRP-Rat) is focusing on collecting, preserving and distributing various rat strains, including spontaneous mutant, transgenic, congenic, and recombinant inbred (RI) strains. To evaluate their value as models of human diseases, we are characterizing them using 109 phenotypic parameters, such as clinical measurements, internal anatomy, metabolic parameters, and behavioral tests, as part of the Rat Phenome Project. Here, we report on a set of 357 simple sequence length polymorphism (SSLP) markers and 122 rat strains, which were genotyped by the marker set. RESULTS: The SSLP markers were selected according to their distribution patterns throughout the whole rat genome with an average spacing of 7.59 Mb. The average number of informative markers between all possible pairs of strains was 259 (72.5% of 357 markers), showing their high degree of polymorphism. From the genetic profile of these rat inbred strains, we constructed a rat family tree to clarify their genetic background. CONCLUSION: These highly informative SSLP markers as well as genetically and phenotypically defined rat strains are useful for designing experiments for quantitative trait loci (QTL) analysis and to choose strategies for developing new genetic resources. The data and resources are freely available at the NBRP-Rat web site 1.

Objects referenced in this article
Strain ACI/NKyo august copenhagen irish Rattus norvegicus
Strain BB/WorTky BioBreeding rat Rattus norvegicus
Strain BN/SsNHsd null Rattus norvegicus
Strain BUF/NacJcl null Rattus norvegicus
Strain DA/Slc dark agouti Rattus norvegicus
Strain DON/Kyo Donryu rat Rattus norvegicus
Strain F344/Stm null Rattus norvegicus
Strain FH/HamSlc fawn hooded rat Rattus norvegicus
Strain GK/Slc Goto Kakizaki Rat Rattus norvegicus
Strain IS/Kyo ishibashi rat Rattus norvegicus
Strain KYN/Hok null Rattus norvegicus
Strain LE/Stm null Rattus norvegicus
Strain LEC/Hok Long Evans Cinnamon Rattus norvegicus
Strain LEW/Seac null Rattus norvegicus
Strain LEW/SsNSlc null Rattus norvegicus
Strain NER/Kyo Noda epileptic rat, GMS Rattus norvegicus
Strain OM/NSlc Osborne-Mendel rat Rattus norvegicus
Strain PVG/Seac Piebald Virol Glaxo Rattus norvegicus
Strain RCS/Kyo royal college of surgeons rat Rattus norvegicus
Strain SHR/Izm null Rattus norvegicus
Strain SS/JrSeac Dahl Salt-Sensitive Rattus norvegicus
Strain TM/Kyo tester moriyama rat Rattus norvegicus
Strain W/Kyo null Rattus norvegicus
Strain WAG/RijKyo null Rattus norvegicus
Strain WBN/KobSlc wistar bonn/kobori Rattus norvegicus
Strain WKY/Izm Wistar-Kyoto Rattus norvegicus
Strain WTC/Kyo null Rattus norvegicus

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