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SNP and haplotype mapping for genetic analysis in the rat

Authors

  • K. Saar
  • A. Beck
  • M.T. Bihoreau
  • E. Birney
  • D. Brocklebank
  • Y. Chen
  • E. Cuppen
  • S. Demonchy
  • J. Dopazo
  • P. Flicek
  • M. Foglio
  • A. Fujiyama
  • I.G. Gut
  • D. Gauguier
  • R. Guigo
  • V. Guryev
  • M. Heinig
  • O. Hummel
  • N. Jahn
  • S. Klages
  • V. Kren
  • M. Kube
  • H. Kuhl
  • T. Kuramoto
  • Y. Kuroki
  • D. Lechner
  • Y.A. Lee
  • N. Lopez-Bigas
  • G.M. Lathrop
  • T. Mashimo
  • I. Medina
  • R. Mott
  • G. Patone
  • J.A. Perrier-Cornet
  • M. Platzer
  • M. Pravenec
  • R. Reinhardt
  • Y. Sakaki
  • M. Schilhabel
  • H. Schulz
  • T. Serikawa
  • M. Shikhagaie
  • S. Tatsumoto
  • S. Taudien
  • A. Toyoda
  • B. Voigt
  • D. Zelenika
  • H. Zimdahl
  • N. Huebner

Journal

  • Nature Genetics

Citation

  • Nat Genet 40 (5): 560-566

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 F(2) 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.


DOI

doi:10.1038/ng.124