Breeding and Maintenance

The aim in maintaining an outbred colony is usually to prevent change. In exceptional circumstances, the aim may be to change the colony in some way, and this can usually be done by selective breeding.

In any colony, genetic change occurs as a result of change in the frequency of alleles at the various genetic loci that are polymorphic in the colony. Within an outbred stock, individual animals will often differ at many thousands of loci. If the frequency of individual alleles changes, then the phenotype of the colony may also change. There are four main causes of genetic change in an outbred stock, as listed below.

Genetic Contamination or Immigration — An outcross is sometimes done deliberately if the breeding performance of a colony declines. However, the introduction of new genetic material may alter the characteristics of the colony. Genetic contamination may also occur by accident if the colony is maintained in physical proximity to another strain or stock.

Mutation — Mutations occur at the rate of about one in 100,000 to one in 1,000,000 per locus, and some of these will become established within the colony, depending on chance and whether or not they are deleterious or advantageous. Recessive genes may be maintained within the colony for many generations, even if they have large phenotypic effects. For example, the Rowett athymic nude rat mutation apparently occurred at some time prior to 1955 in a colony of outbred rats at the Rowett Research Institute in Scotland. It was maintained in the colony in a heterozygous state until 1978, when two heterozygotes were mated and produced hairless young.17

Directional Selection — If the stock is selected for some phenotype such as large body weight, high reproductive performance, or enhanced immune response to some antigen, then the frequency of alleles associated with these characters will change, thereby altering the characteristics of the colony. The rate of change will depend on the strength of selection and the extent to which the character is inherited. Many characters are correlated so that a change in body weight may lead to a change in other characters, such as life span and tumor incidence. Natural selection may also alter some characters. If there is an infection in the colony, those animals, which are most resistant, will tend to produce more offspring so that the frequency of "resistance" genes will increase. If there is a change in husbandry or environment, then those animals that thrive under the new conditions will tend to leave more offspring, and so on. Thus, in order to prevent genetic change, the colony should be maintained as far as possible without directional natural or artificial selection. This is usually achieved by using some procedure for selecting future breeding stock strictly at random, without taking any account of their phenotypic characteristics, though obviously abnormal animals would normally be excluded. If there are major deleterious genes present in the colony, such as blood clotting factors in dogs, then steps should be taken to eliminate affected animals and carriers using progeny testing methods described in many genetics textbooks.18,19 Where single loci have been cloned and sequenced, it will often be possible to develop a PCR-based method for identifying carriers,20 which should make it easy to eliminate them from the breeding stock.

Random Drift — Genetic segregation generates new combinations of genes in an essentially random manner, and in a large outbred stock colony, the frequency of an allele at any given genetic locus should remain constant, according to the Hardy-Weinburg law.19 However, in smaller populations, gene frequency can change simply as a result of chance selection of breeding animals with certain alleles at any given genetic locus. Once an allele becomes fixed in the colony, with all animals being genetically identical at that locus, it will no longer be able to change. The rate of change due to random genetic drift depends on the level of inbreeding, which in turn, depends on the size of the breeding colony and on the amount of genetic variation already present. The coefficient of inbreeding (F) is the probability that the two alleles at a locus are identical by descent, i.e., that they are copies of the same gene at some previous period in the animal's ancestry. F ranges from zero in a colony with no inbreeding to 1.0 or 100% in a fully inbred one. The inbreeding per generation, assuming random mating, is given by the following formula:

AF = 1/8Nm + 1/8Nf where AF is the increase in inbreeding per generation, and Nm and Nf are the numbers of males and females present in the breeding colony, which actually or potentially can leave offspring in the next generation. Note that the rate of inbreeding depends largely on the number of the most numerous sex. For example, if the colony has four breeding males, then the inbreeding with random mating will be

1/32 = 3.1% just from the males' side, however many females there are. This is important when considering colonies of larger animals, such as dogs, cats, and some species of primates, where a few stud males can be used for large numbers of females. In such circumstances, it is often necessary to maintain more males than would normally be needed in order to reduce the rate of inbreeding.

Inbreeding only reduces existing heterozygosity each generation. Over a period of time, the total inbreeding in the colony will be as follows:

where AFt is the inbreeding at generation t, and AF is the inbreeding for the current generation.

If there is a genetic "bottleneck" with a reduced number of breeding animals in one or a few generations, this will lead to an increase in inbreeding that cannot be undone, even if the colony is subsequently enlarged. Formulas taking into account variable sample sizes each generation are given by Falconer.19

Bottlenecks are common when a few breeding animals are used to found a new breeding colony, or when a colony is "cleaned up" following an outbreak of disease. Care must be taken to ensure that enough breeding animals are used.

As a general rule, it is recommended that inbreeding levels should not be more than about 1% per generation if the aim is to maintain the colony for long periods. Table 9.2 shows the inbreeding per generation from colonies maintained with various numbers of breeding individuals, and Figure 9.1 shows the coefficient of inbreeding over a period of 30 generations in colonies of various sizes.

Inbreeding over a period of time, such as five years, can be reduced by having a long generation interval. With mice and rats, it may be possible to have only about two generations per year by saving breeding stock from older females. Breeding from first litters can be avoided. With larger animals such as dogs and cats, there is even more scope for reducing the inbreeding by increasing the intergeneration interval.

A "maximum avoidance of inbreeding" system can also be used with small colonies, which approximately halves the rate of inbreeding. With random mating, on average, each breeding pair will contribute one breeding male and one breeding female to the next generation. However, some animals will contribute more and some less due to sampling variation. If each breeding female and each breeding male were to contribute exactly one female or male, respectively, to the next generation, this will halve the rate of inbreeding relative to random mating. There are various rotational breeding schemes that aim to ensure this happens. One of these is given in Table 9.3. However, in practice, there is little difference between the different rotational breeding schemes.21 All rely on ensuring equal representation of the current generation of breeding animals in the next generation. It is not worthwhile to use a maximum avoidance of inbreeding system if the level of inbreeding is already well below the recommended 1% per generation. Halving something, which is already very small, may not be worthwhile. It is also usual to try to avoid

Table 9.2 Inbreeding with Various Numbers of Breeding Males and Females




Inbreeding after 10

of Males

of Females

per Generation


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