Mapping Data

Experiment

• Experiment
  TEXT-QTL
• Chromosome
  7
• Reference
  J:200665 Kelada SN, et al., Genetic analysis of hematological parameters in incipient lines of the collaborative cross. G3 (Bethesda). 2012 Feb;2(2):157-65
• ID
  MGI:5755449

Genes

Gene	Assay Type
Mcvq4	visible phenotype
Hbb

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 131 male PreCC#/Unc mice from Oak Ridge National Laboratory, identifying five novel loci corresponding to hematological parameters. Each mouse was from a distinct CC line that had undergone five to 14 generations of inbreeding.
  
  Mice were genotyped at the University of North Carolina, Chapel Hill, using one of two Affymetrix SNP arrays (A or B) that were produced in development of the Mouse Diversity array. The arrays contained 181,752 (A-array) and 180,976 (B-array) SNP assays, and the set of SNPs on each array did not overlap. Most mice (83%) were genotyped on the B-array and the remaining were genotyped on the A-array.
  
  Training arrays were annotated to NCBI Build 36 of the mouse genome, but the authors mapped QTL boundaries to Build 37 positions to integrate with other resources. Results are reported relative to Build 37.
  
  QTL Mcvq4 is significant for the trait "Mean red cell volume (MCV)" and maps to 110.34 - 116.24 Mb on Chromosome 7, with a peak LOD score of 20.3 at 111.81 Mb. The authors conclude that Hbb is the causal locus underlying the Mcvq4 QTL.
  
  QTL Mcvq5 is significant for the trait "Mean red cell volume (MCV)" and maps to 8.85 - 22.90 Mb on Chromosome 14, with a peak LOD score of 7.1 at 15.66 Mb. The effects of the NOD/ShiLtJ and 129S1/SvImJ alleles were associated with the greatest MCV. The protein coding gene Anxa7 is proposed as a plausible candidate gene for the Mcvq5 locus.
  
  QTL Wbcq7 is significant for the trait "WBC count (WBC)" and maps to 69.99 - 74.12 Mb on Chromosome 18, with a peak LOD score of 7.1 at 70.65 Mb. The authors report that the 129S1/SvImJ and NZO/HlLtJ alleles were in the low-WBC group and were clearly separate from the other strains.
  
  QTL Ne_pctq1 is significant for the trait "Percent neutrophils/lymphocytes" and maps to 31.29 - 35.19 Mb on Chromosome 11, with a peak LOD score of 9.5 at 32.89 Mb. The NZO/HlLtJ allele effect was distinct from all other allele effects at the Ne_pctq1 locus, and was associated with a greater percent neutrophils/lymphocytes.
  
  QTL Moq1 is significant for the trait "Monocyte number" and maps to 87.56 - 94.96 Mb on Chromosome 1, with a peak LOD score of 7.2 at 92.82 Mb. The authors report that the A/J and WSB/EiJ alleles were clearly associated with low monocyte count.