Rodent Breeding Colonies


Breeding Notes and Guidelines

Collecting Tissue for Genetic Analysis

References and Resources


The intentional breeding of rodents requires IACUC review and approval.  A breeding colony may be necessary to develop an animal model is not commercially available, or produce young animals with specific age or weight that cannot be provided by a commercial breeding colony. Investigators developing a new spontaneous or induced mutant animal model might also need to maintain their own breeding colony because there is no alternative source for the animal model.  Maintenance of a breeding colony must be scientifically justified; cost savings alone is not a valid justification.  

The IACUC has developed policies and guidelines for the maintenance of rodent breeding colonies to assist researchers in minimizing overall animal numbers and potential animal overcrowding while ensuring the most effective breeding activities. 


  • Acceptable breeding schemes for mice include:
    • Paired – one male, one female
    • Trio – one male, two females
    • Harem – one male, three or more females
  • No more than three (3) adult mice may be in a single cage with a litter present.
  • When there is more than one adult female mouse in a cage with a litter or litters, there can be no more than a total of 14 pups.
  • When multiple litters are present in a cage, the age difference between the litters may not exceed 5 days.
  • Due to the increased space requirements, rat colonies are limited to the Paired breeding scheme only, and the male rat must be removed from the cage before the pups are born.
    • The Guide for the Care and Use of Laboratory Animals requires 124 square inches of floor space for a mother rat with a litter; as the standard rat cages currently in use at UCI provide 140 square inches, there is inadequate space for additional adult rats when a litter of pups is present
    • NOTE:  Exceptions to this rule may be considered by the IACUC, e.g., when a particular strain of rat typically produces smaller-than-average litters.
  • Birth dates of all litters must be clearly marked on the cage card; researchers are responsible for providing this information in a clear manner.
  • All litters must be weaned and separated at 21 days of age, unless an exception has been reviewed and approved by the IACUC.
  • Research personnel are responsible for reporting all animals produced in the breeding colony, including animals that are used or held only for breeding and offspring that are euthanized without being used for any research purpose. Animals produced in campus breeding colonies should be reported on the Annual Continuation Application.

Adherence to this Policy

The Lead Researcher is responsible for adhering to this policy and must ensure that all research personnel responsible for colony maintenance are appropriately trained and experienced. Birth dates of all litters must be clearly noted on each cage card.

If significant overcrowding is noted by ULAR staff or campus veterinarians or if a litter is more than 21 days old, a dated "Please Wean/Separate" card will be placed on the cage. Research staff must wean and separate the animals within two (2) calendar days of the posting; ULAR husbandry staff will wean/separate the animals on the third day after the posting, and Lead Researcher will be charged for this service.

Breeding Notes & Guidelines

Researchers are encouraged to keep additional detailed breeding records separate from the cage cards to prevent accidental loss of important data.
Research personnel must provide sufficient monitoring of the animals to prevent overcrowding and deal with associated issues such as cannibalism, fighting, excessively soiled caging, etc. ULAR staff is authorized to separate animals when their welfare is jeopardized by overcrowding or fighting.

Female rodents experience a post-partum estrus and can become pregnant within 24 hours of delivering a litter. Consequently, leaving a male mouse or rat in the cage until the time of delivery can result in the production of a subsequent litter when the first litter is 21 days old.

Significant overcrowding and unintended breeding activity may result if the weanlings are not separated at 21 days of age.

In some circumstances, the cross-breeding of certain transgenic strains with the intention of creating a new strain may require prior Institutional Biosafety Committee review and approval.  IBC review is required if the following conditions are present:

  1. One of the parental rodents requires housing under BL2 (or higher) containment;
  2. One of the parental transgenic rodents contains one of the following genetic modifications: (a) incorporation of more than one-half of the genome of an exogenous eukaryotic virus from a single family of viruses; or (b) incorporation of a transgene that is under the control of a gammaretroviral long term repeat (LTR); and
  3. The transgenic rodent that results from this breeding is expected to contain more than one-half of an exogenous viral genome from a single family of viruses.

For more information, please contact the Institutional Biosafety Committee

Collecting Tissue for Genetic Analysis

Acceptable methods include:

Tail Tip Excision

Surgical removal of the distal tip of the tail (5 mm or less).  Anesthesia is not required for mice 21 days of age or younger, as innervation of the tip of the tail is minimal in pre-weanling mice.  Veterinarians recommend that rat pups undergo this procedure at a younger age; 4-8 days of age is recommended.

Anesthesia is required:

  • For excision of larger sections, or if repeated excisions of tail are required, thus involving the coccygeal vertebrae;
  • If the procedure is performed on weaned animals

Anesthesia can be provided by use of inhalant agents (e.g., isoflurane), injectable agents (pentobarbital, ketamine/xylazine, etc.) and local agents such as cetyl chloride.  Hemostasis must be achieved when performing tail tip excisions, through use of cautery agents such as silver nitrate or a heated scalpel blade. Use of a topical analgesic is highly recommended following this procedure.

Ear Punch

Removal of a small (0.5 – 1 mm) circular section of tissue from the ear pinna, commonly used as an identification method in rodents.    Multiple samples can be collected from one or both ears. Collection of the small tissue samples produced during ear punching may generate enough tissue (DNA) to allow analysis by PCR.  Anesthesia is not required when performing ear punches on rodents.

Peripheral Blood Collection

Veterinary Services can provide more information and training for this method.

Distal Toe Clipping

As a means of identifying genetically modified rodents and collecting tissue for genetic analysis, distal toe clipping (up to the first knuckle) may be used with scientific justification in the approved animal-use protocol.  This method may only be used on neonatal animals (approximately 10 days old or less) and must follow the UCI Transgenic Mouse Facility Standard Operating Procedure for distal toe-clipping in transgenic mice.  

References & Resources

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