Mapping Data

Experiment

• Experiment
  TEXT-QTL
• Chromosome
  2
• Reference
  J:228271 Ram R, et al., Rapid identification of major-effect genes using the collaborative cross. Genetics. 2014 Sep;198(1):75-86
• ID
  MGI:5766275

Genes

Gene	Assay Type
Agoc	visible phenotype
Choq1	visible phenotype
Wbq	visible phenotype
a

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 incipient 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#/Geni mice (110 CC lines from generations N16 and beyond). Mice were genotyped by MegaMUGA (Mouse Universal Genotyping Array) at 77,000 SNP markers and QTL mapping was performed to identify loci related to coat color. All coordinates are relative to NCBI GRCm37 (mm9).
  
  QTL Albc maps to 91 - 96 Mb on Chromosome 7 with a peak located at 93 Mb (LOD score not given) in linkage with albino coat color. The analysis clearly showed that the two albino founders (NOD/LtJ and A/J) contributed to the phenotype. The Tyrosinase (Tyr) gene was identified as the causitive gene. Mutations in Tyr have been functionally validated as causing albino coat color.
  
  QTL Agoc maps to 153.8 - 158 Mb on Chromosome 2 with a peak located at 154 Mb (LOD score not given) in linkage with agouti coat color. The C57BL/6J and A/J founder strains clearly showed allelic differentiation at this locus, with the Agouti (a) gene being the most likely candidate in the region.
  
  QTL Cinq maps to 78 - 81 Mb on Chromosome 4 (peak LOD score and position not given) in linkage with cinnamon coat color. The peak was defined by A/J founder alleles; all strains with the cinnamon trait had the A/J haplotype at the locus. Tyrp1 was identified as the underlying candidate gene; it encodes tyrosinase-related protein, which has been shown to cause the brown color dilution trait.
  
  QTL Choq1 maps to 149 - 156 Mb on Chromosome 2 (peak LOD score and position not given) in linkage with chocolate coat color. The chocolate and cinnamon coat mice shared the same chromosome 4 gene/allele (i.e., Tyrp1). However, all the chocolate coat mice had either a C57BL/6J or an A/J allele at the agouti locus compared to the cinnamon mice, suggesting the non-agouti allele at chromosome 2 interacts with Tyrp1 to produce the chocolate brown coat.
  
  QTL Choq2 maps to 79.5 - 80.5 Mb on Chromosome 4 (peak LOD score and position not given) in linkage with chocolate coat color. The chocolate and cinnamon coat mice shared the same chromosome 4 gene/allele (i.e., Tyrp1). However, all the chocolate coat mice had either a C57BL/6J or an A/J allele at the agouti locus compared to the cinnamon mice, suggesting the non-agouti allele at chromosome 2 interacts with Tyrp1 to produce the chocolate brown coat.
  
  QTL Wbq maps to Chromosome 2 (peak LOD score and locus positions not given) in linkage with the white-belly trait. Only the 129S1/SvImJ haplotype contributed to the allelic differentiation. This strain bears an agouti mutation (Aw) that is known to induce hypo-pigmentation in the belly area. The Wbq locus overlaps the region harboring the agouti (a) gene, making it the most likely candidate gene for the Wbq QTL.