Genetic Background: Understanding its importance in mouse-based biomedical research A Jackson Laboratory Resource Manual This resource manual highlights the importance of using genetically well-defined mice for biomedical research. It briefly describes the following: • The importance of genetic background • Resources for helping researchers choose the appropriate mouse model • Proper nomenclature to communicate the genetic makeup of mouse models • The Jackson Laboratory’s Genetic Quality Control and Genetic Stability programs Cover Photos Front cover, left: JAX® Mice strain C3H/HeJ (000659) Front cover, middle: Technician displaying holders with straws in the liquid nitrogen storage tank in our Cryopreservation Repository. Front cover, right: JAX® Mice strain C57BL/6J (000664) Table of Contents Introduction ........................................................................................................................ 1 Genetic Background Definition and Examples ............................................................................................ 2 Genetic Background Makes a Difference ................................................................. 2 The Influence of 129 Substrain Backgrounds on Targeted Mutations ................. 4 Consequences of Using Inappropriate Backgrounds .............................................. 4 Minimizing the Confounding Effects of Genetic Background .............................. 5 How Substrains Arise .................................................................................................. 5 Resources to Help You Choose Appropriate Models The Mouse Phenome Database .................................................................................. 6 The JAX® Mice Database ............................................................................................. 6 The JAX® Mice Catalog ............................................................................................... 6 JAX Technical Support ................................................................................................ 6 Correct Nomenclature ....................................................................................................... 7 How We Ensure Genetic Quality & Stability .................................................................. 8 Our Genetic Quality Control Program ..................................................................... 8 Our Genome Scanning Service .................................................................................. 9 Our Genetic Stability Program ................................................................................ 10 The Jackson Laboratory: Pioneer in Cryopreservation ........................................ 11 Do Your Part to Lessen the Impact of Genetic Drift ............................................. 12 References .......................................................................................................................... 13 Introduction The utility of the laboratory mouse as a research • Mouse biology databases, such as the Mouse model of human biology is increasing every year. Genome Informatics Database (MGI, Following are some of the reasons: www.informatics.jax.org), the JAX® Mice Database (jaxmice.jax.org), the Mouse SNP Database • The laboratory mouse is biologically similar to (mousesnp.roche.com), and the Mouse Phenome humans, is susceptible to many of the same diseases, Database (www.jax.org/phenome) are continually is easy to maintain, reproduces quickly, and is very being expanded and improved. amenable to genetic manipulation and analysis. • The number of available mouse models, including • The C57BL/6J strain was selected by the Mouse congenics, consomics, recombinant inbred strains, Genome Sequencing Initiative to be the first mouse spontaneous mutants, ENU-generated mutants, strain to be sequenced. targeted mutants, and transgenics, is increasing almost exponentially. • Fifteen JAX® Mice strains, including DBA/2J and C3H/HeJ have been resequenced by the National As the amount of mouse-based biomedical research Institute of Environmental Health Sciences increases, researchers must be more mindful than Resequencing Project (NIH News 2006). Dense ever of the genetic makeup of the models they use. If SNP maps of virtually the entire mouse genome for research is to be reliable and reproducible over time and these strains are available from the Mouse Phenome place, and, most importantly, if it is to have the greatest Database (www.jax.org/phenome). This information potential for improving human health, it must be facilitates comparative genomics among mouse conducted with mice of well-defined, stable, and clearly strains, humans, and other sequenced species. communicated genetic backgrounds. In the following pages, we discuss how these criteria can be met. The Jackson Laboratory 1 Genetic Background Definition and Examples You may occasionally see the following cautionary note on of the targeted mutant strains NOD.129S7(B6)-Rag1tm1Mom/J strain data sheets of some of our JAX® Mice models: (003729) and NOD.Cg-Rag1tm1Mom Prf1tm1Sdz/Sz (004848) is This strain is on a genetic background different from that NOD. However, the first strain carries a targeted mutation on which the allele was first characterized. It should be noted of the Rag1 gene, likely a few Rag1-linked alleles from that the phenotype could vary from that originally described. 129S7-derived ES cells, and possibly some B6 alleles from We will modify the strain description if necessary as published crosses in the strain’s breeding history. In contrast, the second results become available. strain is a congenic (Cg) with more than one donor strain We include this note because the variety of genetic in its breeding history. It carries targeted mutations of the backgrounds and the mutations characterized and published Rag1 and Prf1 genes and possibly some background alleles on them are continually increasing. As a result, researchers from those other strains. Similarly, the genetic background of must be more mindful than ever of the genetic backgrounds transgenic strains FVB/N-Tg(MMTVneu)202Mul/J (002376) of the mouse models they use. and FVB/N-Tg(MMTV-PyVT)634Mul/J (002374) is FVB/N. As applied to a mutant mouse strain, genetic background However, whereas the first strain carries an MMTVneu refers to its genetic makeup (all its alleles at all loci) except transgene, the second carries an MMTV-PyVT transgene. the mutated gene of interest and a very small amount of On the other hand, strains B6.129S7-Rag1tm1Mom/J (002216) other genetic material, generally from one or two other and NOD.129S7(B6)-Rag1tm1Mom/J (003729) each have the strains. As we shall see, that “other” genetic material can same targeted mutation of the Rag1 gene, but on different significantly influence a mutant strain’s phenotype. backgrounds: C57BL/6J (B6) and NOD. Correct strain nomenclature indicates what a mutant strain’s background is. For example, the genetic background Genetic Background Makes a Difference The technology for producing genetically engineered them unexplainable. Such modifier genes are the reason why mice has been substantially refined, resulting in an normal development and physiology often vary significantly ever-increasing number, variety, and availability of mutant among inbred strains. mouse models. Generally, alleles of interest (such as One of the first documented instances of the influence of spontaneous mutations, targeted mutations, transgenes, genetic background on gene expression was the discovery and congenic regions) are maintained on one to several that, on a B6 background, the diabetes (db) and obese (ob) backgrounds that are more vigorous, better characterized, mutations cause obesity and transient diabetes, but, on a more amenable to scientific experiments, reproduce better, C57BLKS/J (BKS) background, they cause obesity and overt display a phenotype better, or have some other advantages diabetes (Coleman and Hummel 1973; Coleman 1978). over other backgrounds. However, alleles are sometimes (Fig. 1, page 3). Since those results were published, genetic transferred to backgrounds that are not well characterized. background has been shown to influence the expression In any case, inattention to a mutant’s genetic background can of many other genes, including the following: seriously confound research results. Each strain has unique background alleles that may interact with and modify the • The multiple intestinal neoplasia mutation (Min) of expression of a mutation, transgene, or other genetic insert. the adenomatous polyposis coli (Apc) gene (ApcMin). The likelihood of such modifier genes having a confounding B6 mice heterozygous for the ApcMin mutation are very effect is especially high in an uncharacterized background susceptible to developing intestinal polyps. Offspring of or in a segregating or mixed background of unspecified these mice mated with AKR/J, MA/MyJ, or CAST mice origin. Even in a well-characterized strain, undiscovered are significantly less susceptible, indicating that the latter modifier genes may confound results, sometimes making three strains harbor strain-unique ApcMin modifier loci, The Jackson Laboratory 2 Genetic Background Genetic Background Makes a Difference (continued) named modifier of Min 1 (Mom1) (Moser et al. 1992; Many phenotypic differences among substrains can Dietrich et al. 1993). The AKR allele of Mom1 has been only be explained by the presence of as yet undiscovered shown to actually