Inbred lab mice are not isogenic: genetic variation within inbred strains used to infer the mutation rate per nucleotide site

Jobran Chebib,Peter D Keightley,Diethard Tautz,Eugenio López-Cortegano,Benjamin C Jackson

doi:10.1038/s41437-020-00361-1

Jobran Chebib, Peter D Keightley + Show 3 more

Open Access

https://doi.org/10.1038/s41437-020-00361-1

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Abstract

For over a century, inbred mice have been used in many areas of genetics research to gain insight into the genetic variation underlying traits of interest. The generalizability of any genetic research study in inbred mice is dependent upon all individual mice being genetically identical, which in turn is dependent on the breeding designs of companies that supply inbred mice to researchers. Here, we compare whole-genome sequences from individuals of four commonly used inbred strains that were procured from either the colony nucleus or from a production colony (which can be as many as ten generations removed from the nucleus) of a large commercial breeder, in order to investigate the extent and nature of genetic variation within and between individuals. We found that individuals within strains are not isogenic, and there are differences in the levels of genetic variation that are explained by differences in the genetic distance from the colony nucleus. In addition, we employ a novel approach to mutation rate estimation based on the observed genetic variation and the expected site frequency spectrum at equilibrium, given a fully inbred breeding design. We find that it provides a reasonable per nucleotide mutation rate estimate when mice come from the colony nucleus (~7.9 × 10−9 in C3H/HeN), but substantially inflated estimates when mice come from production colonies.

Highlights

Inbred mice have long been used for a wide variety of research purposes, ranging from biomedical to behavioral studies (Snell 1956; Boake 1994; Flint 2003; Lilue et al 2019)
FVB/ NRj (FVB) has the highest number of RARA sites, more than 12 times the number observed in BL6
We estimated the mutation rate based on the genome sequences of pairs of individuals from four inbred mouse strains using the site frequency spectrum (SFS) of observed single nucleotide variants

Summary

Introduction

Inbred mice have long been used for a wide variety of research purposes, ranging from biomedical to behavioral studies (Snell 1956; Boake 1994; Flint 2003; Lilue et al 2019). Many important inbred strains used in laboratory studies today are lines that have been inbred by brother–sister mating for over 200 generations, by which time individuals within strains are expected to be homozygous at every site in the genome (Green 1966; Silver 1995). This expectation assumes that no spontaneous mutations arise, which would maintain genetic variation within lines, and that balancing selection does not maintain variation. Even in the absence of balancing selection, inbred lines are expected to maintain an equilibrium level of genetic variation (at mutation-drift balance), which is determined by the mutation rate and the effective population size (Watterson 1975)

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