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Abstract

The genome is in constant evolution. Despite this on-going change, the genome also has to maintain essential functions. Discovering the evolutionary process underlying genome evolution is thus a central goal not only in evolutionary genetics, but also in medicine. I will discuss two studies in the mouse, where we take a systems genetics approach to understand how the genome evolves in the mouse. First I will discuss the evolution of the “Longshanks mouse”, a unique genetic resource created by my collaborator Campbell Rolian at the University of Calgary. By subjecting mouse to twenty generations of strong selection for increased tibia length, he was able to generate mice with 16% longer tibia in two replicated selection lines than their random-bred relatives. We have sequenced genomes of the lines to identify many loci that changed under selection, both in parallel and independently in the two Longshanks lines. By combining population genetics signatures of selection, chromatin profiling and chromosome domain data, we were able to identify 3 candidate limb enhancers at two major developmental regulators, Nkx3.2/Bapx1 and Gli3. Using transgenic reporter assays we showed that a maximum of 13 SNPs in these 3 enhancers contribute to differential enhancer activities consistent with the tibia phenotype. This demonstrates the power of a systems genetics approach to dissect organismal traits to the level of individual basepairs. In a second part I will discuss our novel approach of generating in vitro “crosses” using in interspecific F1 hybrid mouse embryonic stem (ES) cells. Starting from an F1 hybrid ES cell line between Mus spretus and the reference strain BL6 (mostly Mus musculus domesticus), we have developed a simple tissue culture system to generate mitotic recombinants with genome-wide random breakpoints. By bypassing hybrid sterility and inviability, we can now generate “Impossible Hybrid” mouse stem cells and directly investigate which genetic changes underlie species differences. I will present our proof-of-concept results, where we show how to efficiently generate recombinant ES cell lines entirely in vitro without crosses. By coupling in vitro crosses with FACS, I will discuss our forward genetic mapping experiments for cellular traits that are now routine and can be performed in as few as 6 days. This approach will make it possible to create genetic mapping panels of potentially any size from mouse, or indeed human or other mammals with a robust tissue culture system. I will also discuss our perspective on employing advanced organ-on-a-chip and laser-assisted transgenic techniques to obtain tissue or organismal phenotypes from our in vitro recombinant ES cells. In doing so we identify an experimental way towards studying evolutionary systems biology in a mammalian system. Through these two examples I hope to highlight how we envision a new phase for mouse systems genetics in evolutionary and biomedical areas.