The Breeding Toolbox: Inbreeding

First, to tackle the most controversial tool in the breeding toolbox—inbreeding.

The definition of inbreeding is simple. Inbreeding is the practice of mating two closely related animals.

The subject becomes more complicated when breeders try to define how close is “close.” Of course, all animals of the same kind are related, tracing back to a very limited number of ancestors on Noah’s ark. These animals would have inbred extensively for a few generations, but over time they produced enough descendants so remotely related that no breeder would think twice about mating any two of them.

Geneticists have provided breeders with two tools that can be very helpful in measuring how closely animals are related and how inbred they are:

The blood relationship.
The inbreeding coefficient.

Calculating blood relationship is very simple. It is based on the principle that half of any given animal’s genetics comes from one parent and that the other half comes from the other parent. (This principle is a bit simplistic, but good enough for everyday use.) An animal would normally have the following blood relationships to his ancestors:

Parent: 50%.
Grandparent: 25%.
Great-grandparent: 12.5%.

Inbreeding results in closer-than-normal blood relationships. Look what happens below, in the pedigree of an imaginary horse (any similarities to any other horse’s pedigree are purely unintentional). Dust Devil is related to Tornado twice. He receives 50% of his genetics from Tornado as his sire and another 25% from Tornado as his grandsire. Therefore, there is a 75% blood relationship between Dust Devil and Tornado. (Tumbleweed is in turn related to Tornado by a 37.5% blood relationship—half of 75%.)

Clearly, Dust Devil is inbred because he is the offspring of a mare who was mated to her own sire. We can measure this level of inbreeding by using a number called an inbreeding coefficient. Calculating inbreeding coefficients can be complicated in some cases, but there are many software programs available to give you the numbers. If you use pedigree management software, you probably already have an inbreeding calculator handy. A free program is available from Oklahoma State University (scroll down to the calculator called “Inbreeding”). It can be a little finicky, but it works for fairly simple pedigrees.

An inbreeding coefficient basically measures the likelihood of an animal receiving duplicate genes from the same ancestor. In the example above, Dust Devil’s inbreeding coefficient is 0.25, which means he has a one-in-four chance of receiving duplicate genes from Tornado.

But if you thought that Tumbleweed’s inbreeding coefficient would be 0.125, you were mistaken. Tumbleweed is not inbred at all! His dam is not related to Dust Devil or any of his ancestors; therefore, she could not have given Tumbleweed any genes that would duplicate those he received from Dust Devil (beyond what would normally occur in a randomly breeding population of similar horses).

How It Works

Genes are inherited in pairs. One gene of the pair comes from the sire and the other gene comes from the dam.

Frequently there are different varieties, or alleles, of the same gene. For example, the difference between an Angus and a Red Angus is determined by a variation on one pair of genes, represented by the letter b. An Angus steer’s black hair comes from the B allele of the gene, while the Red Angus sports a glossy red coat due to the b allele. So if a Red Angus bull is mated to a Red Angus cow, each will give a b gene to their calf. Its genetic formula can be represented by the letters bb. Likewise, an Angus calf with two black parents will most likely have the formula BB.

But what happen if an Angus bull with the formula BB is mated to a Red Angus cow with the formula bb? Each parent contributes one gene to the calf, so it will have the formula Bb. It will look black like its sire, but it has the potential to produce red calves later on, because it has a red gene. This calf is said to be heterozygous for the black trait, meaning that it has a pair of unlike genes.

Inbreeding tends to reduce the number of unlike genes in a population, particularly when combined with selective breeding. Let’s take the pedigree of our imaginary horse Tumbleweed again, or more specifically that of his sire Dust Devil. Let’s also say that we are working to eliminate the dun color pattern from our bloodline. As with the black gene in Angus cattle, the dun gene in horses comes with two alleles:

D for dun.
d for non-dun.

We plan to use the non-dun (dd) stallion Tornado to eliminate this color pattern. Unfortunately, we are starting out with the dun (DD) mare Cloud to do this. But never fear, we can still accomplish our goal. All of Tornado and Cloud’s offspring will have the same genetic formula (Dd) and will look dun. But suppose we breed Tornado to his daughter Storm Cloud (this is an illustration, not a recommendation). Tornado will always give a d gene to his offspring, but Storm Cloud could provide either a D or a d gene. If these two horses are mated repeatedly over time, a pattern will emerge:

50% of their offspring will be Dd or dun.
50% of their offspring will be dd or non-dun (we will say that Dust Devil falls into this last category).

By inbreeding we have created a population from which we can begin to breed non-dun horses, even though we started with a dun mare. How did this happen? Tornado gave his son Dust Devil one d or non-dun gene. The other d gene came from Dust Devil’s dam Storm Cloud—who in turn got the gene from Tornado!

Applications

Not surprisingly, a common use of inbreeding is to encourage uniformity in a population. Sometimes the idea is to create a whole new breed that will meet a specific set of criteria. Other times the goal is to perpetuate the desirable traits of a given animal, as was demonstrated in the example of Tornado and the d gene.

Another common way that animal breeders use inbreeding is to create two inbred lines or breeds for the purpose of crossbreeding. This practice is very common in agriculture today because it produces dramatic yet predictable results. For example, Angus and Hereford cattle are maintained as separate breeds and then crossed to produce Black Baldies for beef. This use of inbreeding will be explained further in the linebreeding and crossbreeding parts of The Breeding Toolbox series.

A few breeders use inbreeding to test their genetics. Sometimes health problems can lurk in bloodlines without detection for several generations. This is because some genes mask the effects of other genes. Notice that Storm Cloud, in the horse example above, appeared to be dun even though her genetic formula was Dd. The D or dun gene is said to be dominant; that is, it masks the effects of the recessive d or non-dun gene. Intensive inbreeding can be a way to force recessive genetic defects to come to the surface. Unfortunately, this type of experimentation is expensive and takes quite a bit of time. Today DNA tests are becoming available to eliminate the need for this use of inbreeding.

Pitfalls

The ability of inbreeding to uncover detrimental recessive traits is precisely its shortcoming. For example, suppose that, besides the d gene, Dust Devil received two copies of a recessive genetic defect due to inbreeding. Not only would he have to be culled from the breeding program, but so would all of his full siblings, since half of them would display the defect and the other half would carry it. His dam and all of her full siblings would have to be culled, too, because they would all be carriers. Tornado would have to be culled, since he was the original source of the defect. This would mean that most of his relatives would have to go, as well. Unfortunately, breeders are human, and the financial and emotional cost of this type of culling is beyond what most of us can handle. Some carriers usually manage to escape into the breeding program and perpetuate the problem.

Furthermore, there is an interesting phenomenon known as hybrid vigor that inbreeding affects detrimentally. A certain level of genetic variability appears to be needed to ensure the survival of most animal species. Too many like (homozygous) gene pairs are associated with a loss of fertility, immune function, structural soundness, and performance ability.

To avoid these problems, some attempt to limit inbreeding is necessary. Nearly all breeders try to avoid mating siblings to each other or parents to their offspring, but beyond that inbreeding is rather controversial. The question is one of risk. Each breeder must decide for himself how much risk he is willing to accept and how ruthlessly he is willing to cull his breeding stock. This is where the inbreeding coefficient comes in handy. The higher the coefficient, the greater the risk and the more rigorously culling will have to be practiced to ensure the survival of the bloodline.