Mapping Data

Experiment

• Experiment
  TEXT-QTL
• Chromosome
  6
• Reference
  J:229085 Phillippi J, et al., Using the emerging Collaborative Cross to probe the immune system. Genes Immun. 2014 Jan;15(1):38-46
• ID
  MGI:5751891

Genes

Gene	Assay Type
Rabt2	visible phenotype

Notes

• Reference
  The Collaborative Cross (CC) is a large (~1,000 line) panel of recombinant inbred (RI) mouse strains being developed through a community effort (Churchill et al. 2004). The CC combines the genomes of eight genetically diverse founder strains - A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ - to capture nearly 90% of the known variation present in laboratory mice. CC strains are derived using a unique funnel breeding scheme. Once inbred, the RI CC lines can be used to generate thousands of potential 'outbred' but completely reproducible genomes through the generation of recombinant inbred crosses (RIX). The designation 'PreCC' is used to describe a mapping population of CC mice that is still at insipient stages of inbreeding.
  
  CTC (2004), Churchill, G. A., et al.. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet. 36, 1133-7.
  
  
• Experiment
  Linkage analysis was performed on a mapping population of PreCC#/Unc mice using 180,000 SNP markers to identify QTL associated with innate immune system functionality (genome build not given). Ten significant QTL for various immune system traits were identified. PreCC#/Unc mice were derived from 66 independet CC lines, ranging in generation from G2:F5 to G2:F12. QTL were identified using a 1.5 LOD drop interval.
  
  QTL Rabt1 is significant for the trait "ratio of B cells to T cells" and maps to 23.22 - 23.82 Mb on Chromosome 6, with a peak LOD score of 9.49 at 23.46 Mb. The PWK/PhJ haplotype exerts a strong positive effect on B/T cell ratio at the Rabt1 locus, and the CAST/EiJ haplotype exerts a strong negative effect.
  
  QTL Rabt2 is also significant for the trait "ratio of B cells to T cells." It maps to 88.06 - 92.67 Mb on Chromosome 6, with a peak LOD score of 7.33 at 91.38. NZO/HlLtJ haplotype exerts strong positive effect on B/T cell ratio at the Rabt2 locus.
  
  QTL Dccad1 is significant for dentritic cell CD11c antigen density. It maps to 141.62 - 141.65 Mb on Chromosome 7 with a peak LOD score of 8.64 at 141.62 Mb.
  
  QTL Dccad2 is significant for dentritic cell CD11c antigen density. It maps to 136.46 - 138.64 Mb on Chromosome 7 with a peak LOD score of 8.4 at 129.75 Mb.
  
  QTL Tbcq1 is significant for total B cell count. It maps to 23.3 - 23.82 Mb on Chromosome 6 with a peak LOD score of 8.25 at 23.46 Mb.
  
  QTL Bccad1 is significant for B cell CD23 antigen density. It maps to 3.08 - 16.83 on Chromosome 8 with a peak LOD score of 10.96 at 8.64 Mb. 129S1/SvImJ, CAST/EiJ, and PWK/PhJ alleles appear to reduce CD23 antigen density in an antimorphic and incompletely dominant manner. Fcer2a was identified as a candidate gene.
  
  QTL Trmq8 is significant for "Ratio of helper T-cells to cytotoxic T-cells." It maps to 141.14 - 142.25 Mb on Chromosome 7 with a peak LOD sore of 7.15 at 141.65 Mb.
  
  QTL Cd8ts4 is significant for cytotoxic T-cell level. It maps to 141.14 - 142.25 Mb on Chromosome 7 with a peak LOD score of 7.26 at 141.65 Mb.
  
  QTL Ttcq1 is significant for total T cell count. It maps to 23.22 - 23.82 Mb on Chromosome 6 with a peak LOD score of 9.46 at 23.46 Mb.
  
  QTL Trbcq1 is significant for transitional B cell count. It maps to 128.98 - 130.02 Mb on Chromosome 3 with a peak LOD score of 7.84 at 129.76 Mb.