Looking at Old Tools in New Ways: Using Knockouts as Congenics to Study QTLs

A Novel Source of Congenics

It is safe to say that no one has ever entirely removed the flanking genes from an introgressed region by simple backcrossing — even 100 generations yields only an average introgressed segment length of 2 cM (Silver 1995). The problem of flanking regions has complicated analysis of introgressed genes for some time and is of particular concern for the analysis of complex traits using knockouts, (Gerlai 1996) so it is particularly satisfying to see this slightly vexing phenomenon turned to an advantage in QTL (Quantitative Trait Locus) analysis.

In this issue, Bolivar et al. (2001) take advantage of the fact that knockouts are typically generated using ES embryonic stem cells derived from 129 inbred strain and are often backcrossed to C57Bl6 (B6) animals when archived. This convention provides a convenient and growing source of available animals with a small region of 129 chromosome on an otherwise B6 background. The method demonstrated by Bolivar et al. compares the phenotype of B6 animals with the phenotype of B6 animals containing the introgressed 129 region and knockout (B6.129-KO). If there is a difference, the result is followed up with a simple two-part breeding scheme, described in the paper, that separates the effects of the knockout from the effects of the flanking region.

Coverage of the Genome in 129xB6 with Commercially Available Knockouts

One of the most intriguing aspects of the technique developed by Bolivar et al. is the commercial availability of a large number of B6.129-KO strains. Table 1gives names and chromosomal positions for 59 potentially useful knockout/congenics sold by the Jackson Laboratory. At least one knockout exists for every chromosome except 19.

The average coverage of the genome implied by these animals depends on the number of backcross generations. We can, however, determine a range of possible coverage. The overly-conservative assumption that animals …