Inbred mice

Definition and Applications

An inbred strain is one that:

  • is produced using at least 20 consecutive generations of sister x brother or parent x offspring matings, or;
  • is traceable to a single ancestral pair in the 20th or subsequent generation.

All of the standard JAX® Mice inbred strains have far surpassed 20 generations of inbreeding. Except for the sex difference, mice of an inbred strain are as genetically alike as possible, being homozygous at virtually all of their loci. An inbred strain has a unique set of characteristics that sets it apart from all other inbred strains. Many traits do not vary from generation to generation. Other traits are easily influenced by diet and environmental conditions and therefore may vary from one generation to the next. Some inbred strains carry mutations that may or may not be indicated in the strain designation. For examples, C3H/HeJ mice are homozygous for the retinal degeneration 1 mutation (Pde6brd1) and a defective lipopolysaccharide response allele (Tlr4Lps–d), and many inbred strains carry recessive genes affecting coat color. Some of these mutations are cross-referenced in the strain data sheets.

JAX® Mice inbred strains are particularly well characterized:

  • The DNA of 16 JAX® Mice strains has been sequenced: strain C57BL/6J was sequenced by the publicly-funded Mouse Genome Sequencing initiative, and strains 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, BTBR T+ tf/J, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, MOLF/EiJ, KK/HlJ, NOD/ShiLtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ were resequenced by the National Institute of Health and Environmental Sciences (NIEHS) Resequencing Project.
  • SNP data for the 15 JAX® Mice strains included in the NIEHS Resequencing Project are publicly available at the NIEHS and Mouse Phenome Database Web sites;  additional SNP data for many JAX® Mice strains are publicly available at the Mouse SNP Database and the Mouse Phenome Database.
  • The majority of the data in the Mouse Phenome Database is for 40 genetically diverse and widely used JAX® Mice strains.


Substrains are branches of an inbred strain that are either known or suspected to be genetically different from that inbred strain. They form under any of the following three conditions: 1) branches of a strain are separated from the parent colony before the 40th generation of inbreeding; 2) a branch of a strain is maintained separately from the parent colony for more than 20 generations of inbreeding (10 generations in the branch and 10 in the parent colony); and 3) genetic differences from the parent colony are discovered. Unfortunately, the degree of genetic diversity among substrains is often not well characterized.

Research Applications

A limited number of research applications are listed in the strain detail for many of the inbred strains (please refer to Mouse Information Resources). Investigators are strongly encouraged to research the suitability of a mouse model before ordering. The Mouse Phenome Database, an international effort to collect phenotypic data on commonly used and genetically diverse inbred mouse strains, is a valuable resource. It contains detailed characterizations of a wide array of biochemical and behavioral phenotypes for 40 commonly used and genetically diverse inbred mouse strains; it includes hundreds of measurements for phenotypes relevant to human health, including atherosclerosis, gallstones, alcoholism, hypertension, osteoporosis, airway hyperreactivity, pain responses, blood, neurological, behavioral, and sensory disorders, and toxicity to environmental pollutants; it is continually updated with data generated by contributing scientists.