International Mammalian Genome Society

logo18th International Mouse Genome Conference

17-22 October 2004, Seattle, USA


ORAL PRESENTATION

TUESDAY OCTOBER 19

3.00pm – 3.15pm

POLYMORPHISMS PREDATING THE DIVERGENCE OF THE MUS MUSCULUS SUBSPECIES ARE VERY COMMON IN INBRED STRAINS.

Pardo-Manuel de Villena F1, Ideraabdullah FY1, Doherty HE1, Bell TA1, de la Casa-Esperon E2, Detwiler DA1, Sapienza C2

1 Department of Genetics, UNC-Chapel Hill, Chapel Hill, United States, 2 Fels Institute fro Cancer Research, temple University School of Medicine, Philadelphia, United States

We have estimated the total genetic diversity present in a panel of wild-derived and classical inbred strains. Substitutions and microinsertions/deletions generate a variant at 3.5% of the positions in introns and intergenic regions. In coding sequences the frequency of variants is 1.4%, while UTRs have intermediate levels of diversity. Overall microinsertions/deletions contribute 10% to the total number of variant events and 50% of the total number of variant positions. This represents the highest level of diversity described in a mammalian species yet, despite the limited size of this panel. We have classified all variants into two categories depending on whether the variant arose before or after the divergence of the Mus musculus subspecies. Interestingly, 33% of the variants predate the divergence of the subspecies, and a third of those variants predate the divergence of the musculus, spretus and spicilegus lineages. These ancient variants are distributed uniformly across the genome and interspersed within more recent variation. Therefore, a substantial fraction of the diversity is ancient and has been segregating in the ancestral mouse populations for millions of generations.  its an important factor in explaining the levels of diversity found in mouse. Given their frequency ancient variants are expected to contribute significantly to the total phenotypic variation in mouse. These variants, if unrecognized, may affect the topology and length of branches of phylogenetic trees. Furthermore, ancient variants differ significantly from the more recent variants with respect to the patterns and length of linkage disequilibrium and may pose challenges in genetic studies.

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