**2. Recombinant inbred families**

Recombinant inbred (RI) populations are a seemingly simple idea: two inbred strains are crossed, and their F1 progeny are then crossed again to produce an F2. Pairs of these F2 animals are mated, and new lines are established through repeated rounds of sib-mating (**Figure 1A**). By generation F20, we have a population of 99% inbred strains, each of which is a unique mosaic of homozygous genetic regions from both the parents, and for which an effectively infinite set of genetically identical individuals can be produced [24, 25]. This combination of genetic variability between strains but identical genome within strains allows the mapping of linkage between genotype and phenotype. The design has been expanded on in a variety of ways [26], such as increasing the number of parental strains (e.g. the 8 founders used for the Collaborative Cross mice [27, 28]) to increase the number

#### **Figure 1.**

*Production of the BXD family, transgenic crosses, and diallel crosses. Approximately half of the BXD strains are from an F2 (A; epochs 1, 2, 4 and 6), and approximately half of the BXD strains are from advanced intercrosses (AI; B; epochs 3 and 5). Red represents regions of the genome coming from C57BL/6 J (B6), and white represents regions from the DBA/2 J (D2). Solid arrows have been used to represent a single generation of breeding. Trangenic and non-transgenic crosses for QTL mapping can be produced by crossing hemizygous transgenic mice to RI individuals, to produce litters containing both genotypes (C). The transgene is represented in yellow. A diallel cross (DAX) includes all combinations of genotypes, including the inbred 'diagonal', and all reciprical crosses (D). All offspring of the DAX are isogenic, meaning that genotypes are replicable.*

*Recombinant Inbred Mice as Models for Experimental Precision Medicine and Biology DOI: http://dx.doi.org/10.5772/intechopen.96173*

of variants that segregates in the population, or using multiple rounds of crossing before inbreeding, producing so-called Advanced Intercross RI strains (AI-RI) to increase the number of recombinations, and therefore the precision of mapping (**Figure 1B**; [29]). Although RI strains were first developed in mice, and it is mice that we will concentrate on in this chapter, the design has now been used for a wide variety of organisms, including *Arabidopsis* [30, 31]*, Zea mays* (maize) [32], barley [33], *Drosophila melanogaster* [34], *Drosophila simulans* [35]*, Caenorhabditis elegans* [36] and rat [37].

These RI families are an essential complement to data collected in humans, allowing us to build experimental platforms for what is now called precision medicine. Each isogenic RI strain within a family is effectively an immortal genometype. This is important because it allows the same genome to be resampled using any tissue, at any age, with any method, with any environmental exposure or treatment that the researcher cares to use. This allows us to model higher-order genomeenvironment interactions: the many-to-many-to-many problem stated above.

Whereas in human cohorts we have to imagine a counterfactual (e.g. what would have happened had I exercised more?), in isogenic strains we can effectively run this counterfactual – almost perfectly genomically and environmentally matched individuals can be phenotyped with only a single environmental perturbation between them. Even better, we can have multiple duplicates of these identical genome-types within each arm of the study, allowing us to reduce the effect of unwanted environmental perturbations, increasing our power to detect true associations [38]. However, in some sense, this is still an *N*-of-1 study, as only a single genome-type is being used. A problem many pre-clinical studies have had is that all experiments were carried out on a single genome-type and therefore effectively a single individual. The C57BL/6 J strain is often used to represent the entire mouse species [39, 40], when in fact its phenotype can often differ from even the closely related C57BL/6 N strain [41]. This may explain some of the failures to translate effects seen in mice to effects seen in humans, as in these studies only a single (genetic) individual is being examined, and then results extrapolated to the highly genetically diverse human population. RI families overcome this problem – many genome-types can be tested and many replicates within each genome-type. Therefore, we have a high-powered system to detect and test genome-phenome associations.

The goal is accurate genome-phenome prediction. With this goal in mind, we will use the BXD family of isogenic mouse strains as our example of how this can be achieved. The BXDs are by a wide margin the largest and most deeply phenotyped mammalian family and can be used as a testbed for experimental precision medicine.
