title: SNP and haplotype mapping for genetic analysis in the rat.
abstract: 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.
authors.affiliation: Max-Delbrück Center for Molecular Medicine, Robert-Rossle-Strae 10, 13125 Berlin, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Saar
authors.forename: Alfred
authors.initials: A
authors.lastname: Beck
authors.forename: Marie-Thérèse
authors.initials: MT
authors.lastname: Bihoreau
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
authors.forename: Denise
authors.initials: D
authors.lastname: Brocklebank
authors.forename: Yuan
authors.initials: Y
authors.lastname: Chen
authors.forename: Edwin
authors.initials: E
authors.lastname: Cuppen
authors.forename: Stephanie
authors.initials: S
authors.lastname: Demonchy
authors.forename: Joaquin
authors.initials: J
authors.lastname: Dopazo
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.forename: Mario
authors.initials: M
authors.lastname: Foglio
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.forename: Ivo G
authors.initials: IG
authors.lastname: Gut
authors.forename: Dominique
authors.initials: D
authors.lastname: Gauguier
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigo
authors.forename: Victor
authors.initials: V
authors.lastname: Guryev
authors.forename: Matthias
authors.initials: M
authors.lastname: Heinig
authors.forename: Oliver
authors.initials: O
authors.lastname: Hummel
authors.forename: Niels
authors.initials: N
authors.lastname: Jahn
authors.forename: Sven
authors.initials: S
authors.lastname: Klages
authors.forename: Vladimir
authors.initials: V
authors.lastname: Kren
authors.forename: Michael
authors.initials: M
authors.lastname: Kube
authors.forename: Heiner
authors.initials: H
authors.lastname: Kuhl
authors.forename: Takashi
authors.initials: T
authors.lastname: Kuramoto
authors.forename: Yoko
authors.initials: Y
authors.lastname: Kuroki
authors.forename: Doris
authors.initials: D
authors.lastname: Lechner
authors.forename: Young-Ae
authors.initials: YA
authors.lastname: Lee
authors.forename: Nuria
authors.initials: N
authors.lastname: Lopez-Bigas
authors.forename: G Mark
authors.initials: GM
authors.lastname: Lathrop
authors.forename: Tomoji
authors.initials: T
authors.lastname: Mashimo
authors.forename: Ignacio
authors.initials: I
authors.lastname: Medina
authors.forename: Richard
authors.initials: R
authors.lastname: Mott
authors.forename: Giannino
authors.initials: G
authors.lastname: Patone
authors.forename: Jeanne-Antide
authors.initials: JA
authors.lastname: Perrier-Cornet
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.forename: Michal
authors.initials: M
authors.lastname: Pravenec
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Sakaki
authors.forename: Markus
authors.initials: M
authors.lastname: Schilhabel
authors.forename: Herbert
authors.initials: H
authors.lastname: Schulz
authors.forename: Tadao
authors.initials: T
authors.lastname: Serikawa
authors.forename: Medya
authors.initials: M
authors.lastname: Shikhagaie
authors.forename: Shouji
authors.initials: S
authors.lastname: Tatsumoto
authors.forename: Stefan
authors.initials: S
authors.lastname: Taudien
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Birger
authors.initials: B
authors.lastname: Voigt
authors.forename: Diana
authors.initials: D
authors.lastname: Zelenika
authors.forename: Heike
authors.initials: H
authors.lastname: Zimdahl
authors.forename: Norbert
authors.initials: N
authors.lastname: Hubner
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D030541:Databases, Genetic; D016678:Genome; D006239:Haplotypes; D015810:Linkage Disequilibrium; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D051381:Rats / Q000235:genetics*; D011919:Rats, Inbred Strains / Q000235:genetics*; D011995:Recombination, Genetic