Evidence of a large-scale functional organization of mammalian chromosomes





Evidence from inbred strains of mice indicates that a quarter or more of the mammalian genome consists of chromosome regions containing clusters of functionally related genes. The intense selection pressures during inbreeding favor the coinheritance of optimal sets of alleles among these genetically linked, functionally related genes, resulting in extensive domains of linkage disequilibrium (LD) among a set of 60 genetically diverse inbred strains. Recombination that disrupts the preferred combinations of alleles reduces the ability of offspring to survive further inbreeding. LD is also seen between markers on separate chromosomes, forming networks with scale-free architecture. Combining LD data with pathway and genome annotation databases, we have been able to identify the biological functions underlying several domains and networks. Given the strong conservation of gene order among mammals, the domains and networks we find in mice probably characterize all mammals, including humans.



  1. The naming scheme is the original one for SNPs (e.g., 19-058179075-M).
  2. The coordinates are from build 33.
  3. This is the raw file. The analysis program pruned away SNPs based on minor allele frequency and strains based on sister-strain similarity.

Data used for all calculations: snp.strain.33.081604.txt


Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K
PLoS Genet. 2005 Sep;1(3):e33 [ Full Text ] PMCID: PMC1201368

Creek entering the ocean at Sand Beach, Acadia National Park.