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Genetically Diverse Mouse Models for Every Stage of the Research Pipeline

Elizabeth Axton, Ph.D.

Mouse research is often performed in genetically-defined inbred mouse strains, where each mouse within a strain is virtually identical to one another. While controlling for genetic variability can be helpful for mechanistic research, using a single inbred strain may limit the translatability of preclinical experimental findings. Mouse models that incorporate genetic diversity provide new opportunities for translationally-relevant mouse research and expand the spectrum of research applications for laboratory mice. With an expanded portfolio of diversity mouse models, researchers can now choose the diversity option that best suits their research goals at every stage of the research pipeline. Here, we introduce genetic diversity core concepts, provide an overview of the JAX Diversity Portfolio, and present guidelines for choosing a diversity model for your research platform.

Diversity Key Concepts

Genetic diversity can be incorporated into laboratory mouse research in several ways. One approach is to include multiple inbred strains with different characteristics (i.e. C57BL/6J, BALB/cJ). This strategy enables researchers to investigate whether their research outcomes will be consistent in different genetic backgrounds, which is a simple way of determining whether host genetics impact research outcomes. Alternatively, outbred mice that intentionally avoid sibling mating such as the JAX Swiss Outbred (J:ARC) can be used to produce a population of mice with a modest amount of diversity, including randomly segregating heterozygous alleles.

A new generation of sophisticated diversity mice have been developed by breeding inbred strains together with advanced intercross breeding schemes. Recombinant inbred (RI) strains, for example, are generated by first crossing several inbred strains together, then multiple lines are inbred to create a set of new inbred strains. These new RI strains each represent a unique mosaic of the original founder genomes, and thus express unique phenotypes that can be used to answer a broad array of research questions. RI strains range from simple bi-parental crosses such as BXD to more complex multi-parental families such as Collaborative Cross (CC).

Alternatively, crossing inbred strains together and then outbreeding maximizes diversity to create a heterogeneous stock. This is a population of diverse animals with randomly segregating alleles, where each mouse is a genetically unique individual. The JAX Diversity Outbred (J:DO) mice, for example, is a unique platform to test therapeutic interventions in a population that models the diversity seen in a human population.


The JAX Diversity Mouse Portfolio

Here, we present the JAX Diversity Mouse Portfolio. These diversity models were generated with different breeding strategies, which results in different genetic and phenotypic characteristics that can be applied to various research applications.

JAX Swiss Outbred J:ARC

The JAX Swiss Outbred (J:ARC) model is a conventional outbred stock derived from Swiss mouse ancestors. Similar to many other standard outbred mice used in biomedical research, J:ARC is derived from the CD-1(ICR) outbred stock, and has genetic contributions from NMRI/br, FVB/NJ, and SWR/J mice. As a result of outbreeding, J:ARC mice have a low level of genetic diversity and heterozygosity in their genomes. J:ARC mice are commonly utilized when researchers are interested in incorporating a modest level of diversity into their experiments. This diversity, paired with their consistent body weights, make these mice ideal for preclinical safety testing and PK/PD studies of novel therapeutics. Due to their strong breeding performance and ease of care, J:ARC mice are also ideal for IVF and other reproductive strategies and can be utilized as sentinels for health monitoring programs.


The BXD platform is a recombinant inbred panel derived from the C57BL/6J “B6” and DBA/2J “D2” founder strains. BXD has a moderate level of diversity, with 6 million sequence variants across the entire panel of more than 150 unique strains. BXD mice can either be used as individual strains or as a panel of strains. Panels of BXD strains are used to discover new disease phenotypes or traits, or to model a diverse response to interventions. Individual strains may be selected to model diseases, because individual BXD strains express unique phenotypes. With a moderate level of diversity from the two founder strains, BXD mice provide a simple platform to investigate the genetic basis of disease. While BXD mice are suitable for many fields of research, they have been historically used for neurobiology and metabolism research due to the unique phenotypes resulting from C57BL/6J and DBA/2J genetics.

Collaborative Cross (CC)

Collaborative Cross (CC) is a recombinant inbred panel derived from eight founder strains:  A/J, C57BL/6J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, and the wild-derived CAST/EiJ, PWK/PhJ, and WSB/EiJ. This multi-founder breeding strategy resulted in each new RI CC strain having high diversity uniformly across the entire genome, representing more than 50 million sequence variants across the entire panel of more than 50 CC strains. Since each CC strain will have unique characteristics, individual strains provide the opportunity for new disease models and phenotype discovery. Similar to the BXD platform, CC mice are most often used as a panel of strains where researchers select a number of strains and enroll them into their study. Individual strains can then be chosen for additional characterization or testing interventions in follow-up studies. With their expanded diversity, CC strains have historically been used for a broad range of research fields such as immunology, infectious diseases, oncology, neurobiology, and toxicology.

JAX Diversity Outbred (J:DO)

JAX Diversity Outbred (J:DO) mice are a diverse heterogenous stock composed of mice with a mosaic of genetics from the same eight founders as CC strains: A/J, C57BL/6J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, and the wild-derived CAST/EiJ, PWK/PhJ, and WSB/EiJ. Whereas each CC strain represents a fixed and reproducible genotype, each J:DO animal is a unique individual with one of an effectively limitless combination of the segregating alleles. Each individual mouse is genetically unique, and as a population provides the highest levels of genetic diversity currently available in laboratory mouse research. As a whole, the J:DO mouse population is estimated to have over 50 million segregating sequence variants, which is not limited by the number of available strains as seen with CC. J:DO mice are useful for studies that intend to investigate population-wide effects, and can model a wide variety of simple and complex diseases alike. J:DO mice have historically been used in the fields of immunology, infectious diseases, oncology, neurobiology, behavior, and toxicology.


Model Overview Diversity Background Type
JAX Swiss Outbred (J:ARC) Multi-purpose robust mouse with a low level of diversity that can be beneficial for therapeutic testing In Progress Swiss mouse (ICR) Conventional Outbred
BXD RI panel that promotes simple investigation of disease phenotypes, particularly in metabolism and neurobiology 6 million sequence variants 2 Founder Strains: C57BL/6J and DBA/2J Recombinant Inbred
Collaborative Cross (CC) High-diversity RI panel that permits the discovery of translationally-relevant disease models and phenotypes 52 million sequence variants 8 Founder Strains: A/J, C57BL/6J, 129S1/SvImJ, NOD/LtJ, NZO/H1LtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ Recombinant Inbred
JAX Diversity Outbred (J:DO) A highly diverse mouse population that can be used to model the human population, determine genetic causes of disease, assess response to therapeutics Heterogenous Stock


Considerations for Choosing a Diversity Model

Diversity mice are not a one-size-fits-all approach: different diversity models will be useful for different research goals, and some may be better suited for different stages of the research pipeline. JAX recommends considering these points when choosing a strain for various research goals, and referring to the strain characteristics and additional resources to guide your decision.

  1. Confirm that the phenotype is suitable for the study. For many researchers, strain selection will start by determining whether a strain will recapitulate a disease phenotype (e.g. Type II Diabetes, Alzheimer’s Disease, or Leukemia). Phenotypes can also be surgically or chemically induced. Phenotypes for many of the RI strains can be browsed on the Mouse Phenome Database or in the primary literature.
  2. Determine the amount of genetic diversity that is needed. If you are performing mechanistic research, you will likely not need substantial diversity in your study. If, however, you are studying the genetics of complex traits or are modeling a human population, you will need a high diversity population of mice like BXD, CC, or J:DO to achieve your research goals. More information on genetics can be located at the GeDI Resource.
  3. Weigh the importance of reproducibility. RI strains will be reproducible over time and will allow you to continually have genetically consistent individuals. While outbred stocks can be reproducible on a population-wide level, individual mice and genotypes cannot be recreated. This consideration can help you choose between a recombinant inbred strain (CC, BXD) and an outbred stock (J:DO, J:ARC).
  4. Educate yourself on the characteristics of the strain that may require special care. You should be familiar with the strain characteristics to determine if they require special care. For example, individual CC and BXD strains may have phenotypes that result in shortened life spans or impact breeding productivity. Strain characteristics can be found on the JAX Strain Datasheets, or researchers can contact JAX Technical Support for more information.

Contact the diversity mouse specialists ( for guidance on choosing mouse models, designing research studies, and providing JAX services to support diversity research.


GeDI Resource

Mouse Phenome Database

Blog: Diversity Outbred Mice: A Genetically Diverse Mouse for a Diverse Human Population

Blog: The Unexpected Advantages of Outbred Mice in Research

Webinar: Improved Disease Modeling of Diverse Patient Populations with Diversity Outbred Mice