American Fancy Rat & Mouse Association

This article is from the WSSF 2008 AFRMA Rat & Mouse Tales news-magazine.

Breeding – Beyond the Basics: Outcrossing, Line Breeding, Inbreeding

By Nichole Royer & Karen Robbins

* Outcrossing is the breeding together of two animals that are not related to each other.

* Line breeding is breeding together two animals who are related, but not closely.

* Line breeding is the most commonly used breeding method.

* Inbreeding is breeding together closely related animals.

Producing nice pet rats and mice is simple. Producing quality fancy animals is a much more difficult undertaking. Not only do they have to be friendly and healthy, they also need to be attractive to look at, built correctly, and sound.

It is possible to throw two rats or mice together without any thought and produce an animal with good type and beautiful color. It doesn’t happen very often.

One of the things that fanciers love about breeding rats and mice, is the challenge of producing animals who are an improvement on their parents. These breeders immerse themselves in the challenge of researching their animal’s background, finding a mate that not only enhances its good points but improves on its faults, and then breeding the litter to see if the expected outcome corresponds to the expected results.

In doing planned breedings, a fancier always uses one of the two sets of breeding formulas. Each formula is a tool to produce a certain kind of result.


Outcrossing is the breeding together of two animals that are not related to each other in any way. This method of breeding is the least likely to produce any problems, but it is also the least likely to give you significant results.

In its basic form, an outcross is what produces animals that will carry the traits of both parents. Outcrossing is used when new blood needs to be introduced into a line or when a feature in your animals needs improvement and your stock does not have the required feature.

These animals are not bred with their looks in mind, so the outcome is a roll of the dice.

Breeders use an outcross for a very specific reason. If they have a line of rats or mice that excel in all but one of two points, they will look for an unrelated line that consistently produces youngsters who do well in those areas.

The danger of outcrossing is twofold. There is always the possibility that your choice for an outcross will have a fault that your line has never had a problem with. You may have a line of rats that are beautiful, but have square tails. If you bring in an outcross with a beautiful tail, but small ears, you will most likely improve your rats’ tails. You also may discover some time down the line that you are now having problems with small ears.

The other problem with outcrossing is that it is very hard to predict the outcome from breeding. You take your best guess and hope you are correct. Often the characteristics of the resulting offspring vary widely from baby to baby.

Outcross example of Hooded Rat breedings:

Litter A
2 babies have good
size & type, decent
spines, excellent
chest and hood
markings; the rest are
FFR Nut’n Much
Agouti Hooded
Beautiful chest
marking, size, hood,
wide spine, square
type, small ears
One in a Million
Lilac Hooded
Beautiful type, color,
Nut’n Honey
Agouti hooded
Very nice markings,
beautiful chest
marking, small size,
square type, thin tail
KK1652-1 Streaker
Black Hooded
Beautiful type, size,
head, hood, narrow
broken spine, very
poor chest mark
PC Lab Rat-B
P.E. White
Excellent size, type
Lilac Variegated
Good size/type
This litter is the classic example of when an outcross is called for. Nut’n much had a good hood and chest markings, but lacked in type. Since his siblings were similar, as was his mom, inbreeding or line breeding would not have been an improvement. Streaker complemented his faults very nicely. She had the type, but her markings left something to be desired.

Line breeding

Line breeding is the most commonly used breeding method by both novice and experienced fanciers and is a form of inbreeding. When line breeding, you breed together two rats who are related, but not closely. Aunt to nephew, uncle to niece, half brother to half sister, and cousins are all considered line breedings. Breeders of large animals consider line breeding to be when a particular sire or dam is bred upon and appears several times throughout a pedigree.

Line breeding is used to develop a distinctive line of animals. Unlike outcrossing, where you are throwing a bunch of features together and hoping they combine the way you want, line breeding is much more controlled. Because the animals are all related to one another, they are genetically very similar. This means that their offspring will differ much more minimally than those of outcrossed breedings.

The key to line breeding is to pick an animal who is very nice, and who also produced nice youngsters. At various times this animal will have been bred with different females who all had different attributes he did not. In line breeding, you are attempting to combine all the good attributes together while getting rid of the bad ones.

Line breeding example of Hooded Rat breedings:

Litter B
good chest markings,
good markings, good
FFR Nut’n Much
Agouti Hooded
Beautiful chest
marking, size, hood,
wide spine, square
type, small ears
One in a Million
Lilac Hooded
Beautiful type, color,
Nut’n Honey
Agouti hooded
Very nice markings,
beautiful chest marking,
small size, square type,
thin tail
RN Second Edition
Lilac Hooded
Nice type, hood,
spine, mismatched
chest marking
One in a Million
Lilac Hooded
Excellent color/type/
RN & TR Joint Venture
Black Hooded
Good type, adequate
As you can see, the bottom half of the pedigree has nice size, type, and markings. They, unfortunately, do have a consistent problem with mis-marked chests. The top half of the pedigree has type that is not quite as good, but very nice chest markings.


Inbreeding is a technique that has been the most misunderstood by both novice and experienced breeders. It is a tool that can improve a line when used properly or cement problems into a line that are then very hard to eliminate if not used correctly.

Inbreeding’s primary purpose is to bring out all the good points of two animals while bringing to the surface any bad points that can then be eliminated from the line. By inbreeding you will be bringing out any undesirable recessive traits that can then be weeded out from the gene pool you are working with. It is necessary to know what undesirable traits are lurking in the line rather than continually passing them down the generations, only to appear years later when you have established a particular line and may have passed offspring on to other breeders who are then continuing a flawed line making it difficult to eradicate the problem. With all the bad traits eliminated, you can then concentrate on working with all the good features of your animals. The desired result of inbreeding (or line breeding) is to produce animals that are uniform in their features that in turn produce similar results that are always an improvement upon the parents.

In labs, mice and rats have been inbred (brother/sister breedings) for more than 100 generations. These animals are so similar and uniform in their make-up that they are essentially identical to each other. All defects have been bred out and you are left with very healthy, tractable animals. Now, as a show breeder, you would not necessarily want to go about your breedings this way as there is more to breed for than uniformity of the genes. Some fancy breeders have inbred for many generations on their particular color, but it takes great skill and a keen eye to undertake this task.

When inbreeding (or breeding in general), never breed together two animals that have the same flaw and never breed an animal that has only one strong feature and fails in the rest. Any animal you use must have sufficient good qualities overall or you run the risk of setting up a line of mediocre animals that only have one nice feature, say really big ears. Always use your best animals to each other. By breeding only the strongest, healthiest, best examples of their variety can you produce youngsters that meet or exceed the written standards. The key is proper selection of the animals retained for further use in your breeding program and removal from the breeding pool those that do not meet the minimum standards. Serious breeders are very strict in their selection process and make sure any inferior/weak animals are kept from the breeding population.

Serious breeders not only need to select animals with the correct conformation, markings, and color for the desired outcome, but health and temperament must be right up there in their selections. For example, if you have a line of Blue rats that have hemophilia (bleeding issues), you should stop breeding that line. Period. Breeding rats with serious health issues such as this just because their color makes them easy to place into pet homes, is no excuse to continue a flawed line. Not all Blue rats have this issue and new healthy stock must be sought out to work with. After all, no pet owner wants to have their pet rat bleed to death because it ripped off a toenail or a fellow breeder be told not to breed their rat more than once or it may die delivering a litter.

Responsible breeders will discontinue a line if they discover it produces a major defect. They will also cull from their breeding program any animals that don’t meet their goals, whether that is by keeping undesirable offspring themselves or humanely euthanizing any with health or temperament problems. Many breeders will place into pet homes animals that are not suitable for breeding, but even with a contract signed by the pet owner does not mean that that animal will not be bred either by accident or on purpose, thereby continuing a flawed line that you tried so hard to stop. Some breeders think that if they don’t inbreed, then there won’t be a bad trait to worry about, not realizing that if the trait is recessive, it will be carried down the line for many generations.

But that does not mean health and temperament are the only things to breed for whereby you ignore conformation. Also, selecting only color or markings and not the other important points of the animal, are not the reason to breed as well. The show community is seeing far too many rats with mild to serious structure (conformation) issues and these rats are continually being bred by pet breeders whose only goal is to make more rats of a pretty sellable color, marking, coat, or body type. This is an example of how you can “fix” bad traits into a line—breed poor type to poor type and you may have animals that have beautiful color or markings, and make nice pets, but seriously lack the body to go with it. Judges have also seen far too many rats with aggression on the show bench from breeders who say they breed for temperament. These animals must never be bred upon and their background must be seriously studied to try and determine if this is happening within the line so it can be eliminated.

With more and more casual breeders getting into breeding rats and mice, we are seeing more and more inferior, weak animals and the continuation of serious health and temperament issues being sold as pets and to other casual breeders. These breeders do not understand nor research breeding and genetics for their particular animal and get culls (animals sold strictly as pets) or pet shop animals that should not be bred in the first place. They also do not understand culling or stopping a line when necessary and the importance of keeping inferior individuals out of the breeding population. They hear the term “cull” and their only knowledge on the subject is cutting back a litter at a young age that is done for the health and betterment of the mom and remaining babies—to them babies should never be killed for any reason even if they have something wrong with them. They don’t realize that culling is just eliminating from the breeding population, whether it is at a young age or later when weaned babies are sold strictly as pets or the breeder keeps back any questionable ones themselves rather than run the risk of “pet only” ones being bred, especially if there are health, temperament, or structure issues that have shown up in the line.

Inbreeding is necessary when you have an animal with a desired new trait. This new trait must be unique from anything already accepted before you continue to try and perpetuate the feature. You must also consider if the new feature is something that should be perpetuated. After all, it may be something unique, but if it is harmful in the physical structure or health of the animal to where these animals will suffer because of it, it should not be continued. If the trait is recessive, you must inbreed to get more of the new trait, either by brother/sister breedings, or parent with the new trait to offspring. Occasionally a new trait will pop up in a breeder’s stock so they have the parents and siblings to work with to create more of the new trait. Oftentimes though, a new trait is discovered in a pet shop, rescue center, or other place, so obtaining relatives is not possible and you are left with only the one example of the new feature to work with. Most new traits are recessive, thereby making it imperative that inbreeding be done to make more of the new feature, if it is reproducible.

There is much misconception about inbreeding and what it does. Most breeders believe that inbreeding will cause major deformities, dramatic health problems, infertility, or other issues. If you inbreed and these problems arise, that is because the problems were already present in the line and have become visible. If you didn’t inbreed, these traits would be passed down the line to only occasionally surface. Only by inbreeding and then eliminating any stock that has serious issues or stopping a line when a major health problem or defect comes to light, can a breeder then continue their work on producing an animal that not only has the correct conformation, color, markings, coat type, etc., but also has the health and temperament to go with it.

Inbreeding is not for everyone. It requires research into the backgrounds/pedigrees of the animals you are breeding, knowledge of genetics, and knowledge of the written standards you are breeding towards. You also need to know how to interpret the standards and seeing what an ideal specimen looks like that meets the standards, is important.

Record keeping is a must when doing any kind of breeding, not only to keep track of the colors and markings, etc., of the offspring produced, but also details of the type, temperament, and health attributes of the litter so you know how you are progressing in your breeding program and when an outcross is necessary.

Serious fanciers use inbreeding as a tool to improve a line of animals which they have been working on for many years. With these many years of breeding experience, they know their animals, and know what they are likely to produce.

So whether you breed a few litters or a lot, you will use one of these breeding methods at some point. The stock you obtain from other breeders may have been heavily line bred or inbred and it is important to know how and why each method was used. Each one has a time and place for their use to obtain the desired results. Breeding animals is more than just placing two together and waiting for the babies to come. It takes skill and patience to produce animals that excel in all parts and are an improvement on their parents. Remember, quality, not quantity. Are you up for the challenge? *

Glossery of Terms:

  • Outcrossing – to breed animals that belong to different strains of the same breed
  • Line Breeding – selective breeding to perpetuate certain qualities or characteristics in a strain of stock
  • Inbreeding – to produce by the continued breeding of closely related individuals
  • Culling – to pick out from others, select

Suggested Reading:

Practical Inbreeding by W. Watmough. Fur & Feather/ Watmoughs Publishing Ltd.

Colour Inheritance in Small Livestock by Roy Robinson. 1978. Fur & Feather/Watmoughs Limited. ISBN 0-903775-06-9.

AFRMA Rat Genetics book, 2nd Edition, 2007.

AFRMA Mouse Genetics book, 4th Edition, 2007.

AFRMA Breeding Book, 3rd edition, 2007.

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Updated March 18, 2014