SNP and haplotype mapping for genetic analysis in the rat.
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.
Max-Delbrück Center for Molecular Medicine, Robert-Rossle-Strae 10, 13125 Berlin, Germany.
Saar
Kathrin
K
Beck
Alfred
A
Bihoreau
Marie-Thérèse
MT
Birney
Ewan
E
Brocklebank
Denise
D
Chen
Yuan
Y
Cuppen
Edwin
E
Demonchy
Stephanie
S
Dopazo
Joaquin
J
Flicek
Paul
P
Foglio
Mario
M
Fujiyama
Asao
A
Gut
Ivo G
IG
Gauguier
Dominique
D
Guigo
Roderic
R
Guryev
Victor
V
Heinig
Matthias
M
Hummel
Oliver
O
Jahn
Niels
N
Klages
Sven
S
Kren
Vladimir
V
Kube
Michael
M
Kuhl
Heiner
H
Kuramoto
Takashi
T
Kuroki
Yoko
Y
Lechner
Doris
D
Lee
Young-Ae
YA
Lopez-Bigas
Nuria
N
Lathrop
G Mark
GM
Mashimo
Tomoji
T
Medina
Ignacio
I
Mott
Richard
R
Patone
Giannino
G
Perrier-Cornet
Jeanne-Antide
JA
Platzer
Matthias
M
Pravenec
Michal
M
Reinhardt
Richard
R
Sakaki
Yoshiyuki
Y
Schilhabel
Markus
M
Schulz
Herbert
H
Serikawa
Tadao
T
Shikhagaie
Medya
M
Tatsumoto
Shouji
S
Taudien
Stefan
S
Toyoda
Atsushi
A
Voigt
Birger
B
Zelenika
Diana
D
Zimdahl
Heike
H
Hubner
Norbert
N
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