International Mammalian Genome Society

The 16th International Mouse Genome Conference (2002)

Plenary Presentations * Oral Presentations *
Poster Presentations: Complex Genetics and Disease Modifiers * Developmental Genetics * Functional Genomics * Gene Discovery * Genetic Manipulations to Alter Gene Function * Mouse Models: Human Disease and Pharmacogenetics * Sequence Annotation and Comparative Analysis of Genomes *
Attendees * Sponsors * Table of Contents * Photographs * Awards

POSTER 30 - A FULLY INTEGRATED, HIGH DENSITY PHYSICAL AND GENETIC MAP FOR QTL MAPPING IN CxB RECOMBINANT INBRED MICE

M. T. Pletcher
The Scripps Research Institute

2)Hogenesh J, 1,2) Kay S, 2) Wiltshire T
1) The Scripps Research Institute 2) Genomics Institute of the Novartis Research Foundation

Use of recombinant inbred (RI) mice allows for the mapping of genes affecting multiple and widely varying phenotypes without requiring new genotyping data for each mapping exercise.  Therefore, a detailed map of strain distribution patterns for RIs linked to physical chromosomal positions provides a resource that rapidly define candidate regions for quantitative trait loci (QTL) of any phenotype characterized in the mice.  We have typed all 13 publicly available CxB RI strains with 505 single nucleotide polymorphism (SNP)-based markers and combined the new data with the existing genotype data from another 845 genetic markers.  Sequence for the 1350 markers, roughly one marker every 2MB, were compared against both the Ensemble and Celera genomic sequence assemblies and ordered accordingly.  The combined genetic/physical map contained an additional 57 strain distribution patterns compared to the older data set.  As a test of the integrated map, previously described phenotype data for differences in the ratio of light:dark activity rates in CxB RI strains was applied and a 4.35 MB region on chromosome 19 was indicated as having a negative correlation with a p-value of 0.00097.  Using the Gene Expression Atlas (http://expression.gnf.org/circadian/), 5 genes were identified within this region as being expressed in a cyclical manner consistent with a role in circadian locomotor activity.  Further analysis is underway to determine if any of these candidate genes contain strain-specific polymorphisms and if those alterations result in a functional consequence.