There are many different systems of breeding. The main difference between them is the degree of difference in the relationship between the parents. The extremes are cross breeding where the parents are totally unrelated to each other and inbreeding where the parents are closely related to each other. When two animals belonging to the same breed are mated, this is called Pure Breeding. When two animals belonging to the same breed and registered with the Breed Society are mated, this is called Pedigree Breeding.

Two of the techniques used in Pure Breeding are Inbreeding and Line Breeding.


This is the mating of animals of the same breed that are more closely related than the average of the breed.

Over the years an element of fear has developed over the dangers of inbreeding. The marriage laws for people are designed to prevent marriage of extremely close relations. However, inbreeding does have its uses, and it has played a large part in the establishment of some degree of uniformity in the breeds of livestock, which are on farms today.


Close Breeding which is the mating of:

  •     Father to Daughter
  •     Mother to Son
  •     Brother to Sister

Brother and Sister have on average half their genes in common. Father and Daughter or Mother and Son also have half the genes in common.

Line Breeding is the mating of:

  •     Half Brother and Half Sister                           
  •     Half Cousins                         
  •     Grandfather to Granddaughter                        
  •     Cousin to Cousin                       
  •     Grandson to Granddaughter


The genetic effect of inbreeding is that it makes more pairs of genes homozygous.

Percentage of homozygous genes after the stated number of generations of inbreeding
Self-Fertilisation (Plants)50%87.5%99.9%100.0%
Brother and Sister25%50.0%88.6%98.6%

This means that, in the case of plants which are self-fertilized, after 20 generations of mating, all the genes in the offspring will be homozygous – there will be no recessive in the genotype.


Increasing the degree of homozygous, ‘inbreeding’ increases the chances that recessive genes will come together and be homozygous. Some of these recessives may control lethal detrimental characteristics. (Note inbreeding does not increase the frequency of these genes, but increases the chances that they will come together).

Inbreeding does not uncover dominant genes because they always show themselves. However, it increases the degree of homozygosis among the dominant genes. Thus inbreeding can help to fix characters within a breed, but at the same time as fixing good characters it may help to fix bad ones.

On the surface it seems simple to cull the animals showing the bad characters and keep the good animals. However, the cost of such a culling programme in cattle, and even in pigs and sheep, would be prohibitive in most circumstances because, so many animals would have a mixture of good and bad characters (although both would be in the homozygous form). Close inbreeding is rarely practiced for these reasons.

Examination of the effects of inbreeding on quantitive traits have been studied especially in pigs. These studies have conclusively shown that increased inbreeding produces a decline in those traits related to physical fitness. Some of these traits include fertility, viability and early growth rate.

One generation of brother sister mating reduce litter size by one, and three generations of such a mating will reduce it by two.

Inbred animals within a specific inbred line are more likely to be alike genotypically than phenotypically for traits of economic importance. Many pigs in highly inbred lines are quite variable in size and weight at pork weight. Cross-bred litters may well be more uniform and more easily marketed. Much of this difference is due to the unfavourable way in which inbreds react to their environment. This difference is due to the crossbred being better buffered against the adversities of environment.

Some farmers still recommend inbreeding to fix characters in an outstanding strain. Inbreeding couldhowever result in decreased performance and the strain could die out. Furthermore, the farmer loses the chances of introducing new ‘good’ genes if he restricts himself to inbreeding.

It is a fact that crossing two members from different inbred lines can produce remarkably good, uniform animals, and this is the basis of hybrid production in pigs and poultry.

Inbreeding has its value, but must be carefully conducted and will be extremely expensive.

Figure 1: An Example of Inbreeding

  •     E and G: These are full brothers
  •     F and H: These are full sisters
  •     I and J: These are full cousins. The result of crossing these two cousins is K. This is inbreeding, but it is not close breeding nor is it true line breeding.


Line breeding is a less intensive form of inbreeding than close breeding.

The objective of line breeding is to keep the offspring related to an outstanding animal, usually male, which had the desired characteristics. It aims to avoid some of the dangers attendant with close breeding.

Figure 2: Example of Line Breeding

  •     G and I are half-brothers and H is their half-sister.
  •     K and L are half cousins.
  •     K has 50% of his genes from A and 25% from B and C.
  •     M can be traced back to A through three lines, and is line bred to A. The Concentration of A’s genes in M are much higher than if A had only appeared once in the ancestry.
  •     It can also be seen that outside or ‘new’ genes have been introduced through E and F, and this introduction of outside genes is not possible with close breeding.


Line breeding is useful when an outstanding sire has been found and proved by progeny tests. He himself may be used for a second or third time along the line if he is still living, and he belongs to the farmer. The line breeding system must be carefully designed by a person who understands the implications. It is not a system for the commercial herd and is possibly best left to the outstanding herd when the purchase of an outstanding sire to provide genes better than those in the herd is impossible.


  •     It keeps an offspring related to an outstanding animal, usually male, which has desirable characteristics;
  •     It avoids the dangers of close breeding;
  •     It permits the introduction of some new genes to the herd;
  •     It must be practiced in a herd large enough to support at least two sires, or by using Artificial Insemination. Otherwise there is a danger of close breeding;
  •     It is usually carried out in an outstanding herd, where it is not possible to purchase a sire from outside the herd that would provide better genes than those already in the herd; and
  •     It must be carefully worked out by someone who understands the full implications of the system.


  •     In breeding does not create fresh genes but it does sort out the genes already in the gene pool of a herd. It increases the number of genes in the homozygous condition;
  •     Most undesirable traits such as lethal bulldog calves are recessive. These can be discovered and brought out into the open by close breeding;
  •     Close breeding such as a mating between sire and daughter will test the good and the bad genes in that family. Such mating is used on an experimental basis to discover if there are any undesirable recessives in the family, such as red coat colour in Friesians. Once the results of such a test mating are known, the breeder has a much better idea whether to use the sire for a line breeding programme;
  •     There is no point in line breeding to a bad sire;
  •     The transmitting qualities of a sire will be affected if he is inbred. An inbred sire is much more likely to be prepotent, than a sire bred from unrelated parents. Some farmers and breeders have been fortunate in having few undesirable recessives in their herds, and certain inbred sires and dams have been very pre-potent for high production, particularly milk production. The development of several lines; or families within a herd has produced some outstanding animals when these lines have been crossed; and
  •     There are many advantages of inline breeding to a good sire, as the inbreeding will, emphasise the good traits as well as the bad traits that the sire is transmitting.


The main disadvantage of inbreeding is inbreeding depression, and this varies with the breed of animal and the merit of the sires used. In dairy cows, the average drop in milk yield is 20 litres per lactation for every 1% of inbreeding.

The loss of milk yield is due to the general depression that affects all in bred animals. The following are affected, in the order shown:

  •     Milk Yield
  •     Fertility
  •     Rate of Maturity
  •     Live Mass
  •     Disease Resistance
  •     General Health
  •     Conformation

Milk yield is the most affected, and type and conformation (appearance) are least affected so that type can be fixed most speedily by inbreeding.

In any mating, there is a strong tendency for the offspring to move towards the breed average – the pull to breed average that we discussed when talking about natural selection in lecture 5. This is particularly so in the case of traits which have a low heritability, such as milk production. Over the past 20 years, the breed average figures for milk production have gradually been rising, but the process is very slow. Much of that rise is not due to genetic factors, but has been caused by:

  •     The tendency to select from the top half of a breed for breeding purposes; and
  •     Great improved feeding and management of the cattle in the breed.

Regression works both ways and below average stock will tend to rise to the breed average while above average stock will tend to fall to the breed average. The main reasons for regression are:

  •     Two extreme types, that is extreme in the same way, are unlikely to be mated together. Under a system of random mating, two very good animals are unlikely to be mated together and two very bad animals are unlikely to be mated together;
  •     An animal that performs well is not necessarily going to transmit well;
  •     A sire that is prepotent does not transmit this to his offspring; and
  •     Improved performance due to Heterosis or Hybrid Vigour is seldom transmitted.

Normal regression applies to all the traits that are quantitive (i.e. can be weighed and measured) rather than to the traits that are qualitative (horns; coat color etc.)  This is because the qualitative traits are controlled by single genes or simple gene pairs, while the quantitative traits are controlled by large and complex numbers of genes – linkage groups of genes. These linkage groups are more easily brought down to breed average.

In the case of inbred animals, the inbred females show inbreeding depression more strongly than normal regression, and tend to perform worse than one would expect after allowing for normal regression. Inbred males show the advantages of greater purity and are more prepotent than one would expect, after allowing for normal regression.

Crossing two lines that are inbred but unrelated often shows a complete disregard for regression. The females may be better performers than the best parent. This is because the inbred lines have been selected for purity for a number of desirable, dominant traits. Bringing two such lines together will result in all the desirable dominant traits being expressed in the offspring.