Subspecific origin and haplotype diversity in the laboratory mouse
Resource
NATURE GENETICS, 43(7), 648-655
Journal
Nature Genetics
Pages
648-655
Date Issued
2011
Date
2011
Author(s)
Yang, Hyuna
Wang, Jeremy R.
Didion, John P.
Buus, Ryan J.
Bell, Timothy A.
Welsh, Catherine E.
Bonhomme, Francois
Yu, Alex Hon-Tsen
Nachman, Michael W.
Pialek, Jaroslav
Tucker, Priscilla
Boursot, Pierre
McMillan, Leonard
Churchill, Gary A.
Abstract
Here we provide a genome-wide, high-resolution map of the phylogenetic origin of the genome of most extant laboratory mouse inbred strains. Our analysis is based on the genotypes of wild-caught mice from three subspecies of Mus musculus. We show that classical laboratory strains are derived from a few fancy mice with limited haplotype diversity. Their genomes are overwhelmingly Mus musculus domesticus in origin, and the remainder is mostly of Japanese origin. We generated genome-wide haplotype maps based on identity by descent from fancy mice and show that classical inbred strains have limited and non-randomly distributed genetic diversity. In contrast, wild-derived laboratory strains represent a broad sampling of diversity within M. musculus. Intersubspecific introgression is pervasive in these strains, and contamination by laboratory stocks has played a role in this process. The subspecific origin, haplotype diversity and identity by descent maps can be visualized using the Mouse Phylogeny Viewer (see URLs).
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journal article
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