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inbreeding diversity pedigree linebreeding genes genetics dog crossbreeding outcrossing animal husbandry Fred Lanting

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INBREEDING AND DIVERSITY - PART 2

by Fred Lanting

Copyright January, 2009 -

Continued from PART 1

Two types of problem generally arise when inbreeding is practiced in a population: an increase in the occurrence of deleterious recessive traits, and inbreeding depression.  When inbred animals mate, the level of homozygosis in the population increases. This leads to a higher probability that deleterious alleles will appear in the same individual. In the German Shepherd Dog, somewhat common “simple”-recessive traits include long coat, progressive retinal atrophy and pituitary dwarfism.  Other problem traits such as hip dysplasia (HD) are polygenic, and not as sensitive to homozygosis (homozygosity) at individual loci, but are also expected to increase with higher levels of inbreeding. Inbreeding depression is a decrease in quality or performance of inbred animals that is due to the expression of unfavorable genes affecting polygenic traits. The traits most affected are traits such as fertility and survivability, which have a negative effect on lifetime health and performance. Close inbreeding should be carefully avoided to prevent such problems. In livestock breeding, 6.25% is often used as an upper limit for an acceptable level of inbreeding in a population. This is not always the case, and should not automatically be assumed as a limit for dogs, but is a good starting point to consider.

There is a mathematical measure of inbreeding that is similar to that used for relationship.  The coefficient of inbreeding, denoted FX  where “X” is the name of the individual in question, is the probability that two genes taken at random from an individual are identical by descent.  FHoratio in Figure 2 is 0.25 (25%), which implies that genes are identical by descent at 1 of every 4 of his loci. Such a high degree of inbreeding is almost certainly undesirable. Equations to predict the inbreeding coefficient of any individual (given a pedigree) have been derived, but we shall not discuss those here. Coefficients of inbreeding for some common matings are presented in Table 2, and you can see the similarity to Table 1. The method mentioned earlier for calculating relationships in small pedigrees also yields the coefficients of inbreeding for all animals in the pedigree.

Table 2.    Coefficients of Inbreeding for Some Common Matings

You may now be anxious to point out that all members of a breed, and perhaps even a species, are related to one another. This potential problem has long been recognized, and to get around it, we define what is called a genetic base. This base is simply an arbitrary population that is assumed to be non-inbred. For example, the base might be assumed to be all dogs born in 1950. It must therefore be emphasized that FX has meaning as a measure of inbreeding only relative to a base population. If we defined Vincent and Emma’s generation as the base in Figure 2, then Horatio would have a coefficient of inbreeding of zero. The idea is not that inbreeding never occurred before that point, but that it occurred far enough back in time that it would not have a significant influence on the current population if inbreeding is avoided or carefully managed in the future. To illustrate the point, the average relationship between an individual and an ancestor eight generations back in their pedigree is only about 0.00391 (0.391%).

Comparing Relationship and Inbreeding

It is necessary to take a moment to stress carefully the differences between coefficients of relationship and coefficients of inbreeding.

RXY      measures the proportion of an animal’s genes that are identical by descent to those of a second animal; relationships can exist in the absence of inbreeding.

FX        measures the proportion of an individual’s genes that are identical by descent to one another; remember that inbreeding does not exist in the absence of relationship.

It may help to think of relationship as a characteristic of a pair of individuals, while inbreeding is a characteristic of an individual. As will be demonstrated in an example later, two unrelated, inbred individuals may be mated to produce an individual that is not inbred. It is simple to understand this if the differences between inbreeding and relationship are kept firmly in mind.

The Tabular Method for Calculating Relationship and Inbreeding

The advantage of the tabular method of calculating relationship and inbreeding is that it is much simpler to use than the so-called path method. It can become tedious to do by hand if there are a large number of animals in the pedigree you are interested in, but can easily be programmed into a spreadsheet for your computer to deal with. Since we do not know anything about a given offspring, we shall refer to him/her as “X”.

Figure 3.   A Mating Between Bob and Victoria

The first step is to set up the pedigree containing the individuals of interest. A common situation might be the examination of a mating between Victoria, a full sister of Horatio, and the Bob of the example in Figure 3 above.  We shall refer to the offspring of this mating as “X”.  This pedigree will be used to demonstrate how to easily figure out coefficients of relationship and inbreeding.

We are going to construct a table with as many rows and columns as there are unique animals in the pedigree. In Figure 3 there are ten animals, but Emma appears twice, so we will construct a 9-by-9 table. The animals in the pedigree should be ordered by generation from oldest to youngest. For example, we would order X’s pedigree like this:

Edmund, Emma, Tom, Annie, Jack, Vincent, Bob, Victoria, X

The animals are alphabetized within generation, but this is not necessary. When an individual appears in successive generations, as Emma does, assign her to the group in which she first appears. A given entry in the table is the relationship between the individual at the top of that column and the individual at the far left of that row.  Once the table is drawn out, the names should be filled in like this (and we will add more later, below Edmund, in subsequent steps):

Table 3 a.

In some cells, such as Jack’s, there are two or three names. The lower names, which I have highlighted in boldface, are the animals the columns correspond to. The upper animals are the parents of that animal. We need this information close at hand to fill in the table.  There will also be a row for each dog in the pedigree; the table has been abbreviated here in step 1 to save space. We will demonstrate how to fill in the table, one row at a time, in a series of four steps. I have used some abbreviations in the table to save space: Edm is Edmund;  Em is Emma;  Ann or An is Annie; Vinc is Vincent; etc.

The Row ‘Edmund’

The first cell in the table corresponds to Edmund’s relationship to himself, which will be 1 unless Edmund is inbred.  Since we do not know who the parents of Edmund are, we assume he is not inbred and write in a ‘1’.  The second cell is the relationship between Edmund and Emma.  From the pedigree, we see they are unrelated, and write in a ‘0’; we do this for Tom and Annie as well.  To find the relationship of Edmund to Jack, look in the cell for Tom in this row and divide that value by two (because Jack got half of his genes from Tom), which is ‘0’.  The procedure for Edmund and Vincent is similar: look at the entry for each parent, divide the number by two, and add them up.  For Vincent, we have ½ + 0 = ½.  For Bob, we get 0 + 0 = 0, which you can confirm by looking at the pedigree.  Victoria is the grand-daughter of Edmund, so they share a quarter of their genes in common.  For X, we find 1/8 + 0 = 1/8.

Table 3 b.

If you are confused or uncertain about the value you have calculated for an entry, look at the pedigree.  If you have a large number, but there are many steps between the two animals, you may have made an arithmetical error.  The number in the cell should always make sense when compared to the pedigree.

The Row ‘Emma’

Now that we have added a second row to form a column, a comment is in order that will greatly reduce your labor. Look ahead to the completed Table 3 e, for a moment. If you draw a diagonal line down the matrix from the cell Edmund-Edmund to the cell X-X, the numbers above that line will be the same as the numbers below that line. The diagonal is darkly shaded in the completed table in Table 3 e (step 4 of this Bob-Victoria breeding exercise). The shaded upper-right “triangle” in the completed table can be flipped around the diagonal axis to fill in the lower part of the table. The row for Edmund contains exactly the same entries as the column for Edmund. So to get started, we copy the entry from Edmund-Emma into Emma-Edmund, which is ‘0’.  The rest of the entries follow as in step (1):

Since Emma is “related to herself” (“has the same genes” is another way of saying this) by a factor of one, look across her row and see who else she is related to. To Vincent, it is 1 (herself as one of the parents) divided by 2 (since she is only one of the two parents.) In the same way, relationship to Victoria is calculated by dividing 1.5 (½ for Vincent’s R value and 1 for her own as Victoria’s dam) by 2, to give the ¾ you see in the table. Emma has no relation to Bob because she has no relation to his parents Jack or Annie (therefore 0/2 in each case).

And now, back to where we were, in the early stages of constructing that coefficient of inbreeding Table 3:                               

Table 3 c.

We continue to build our table. Remember that for convenience more than anything else, we put the oldest ones on the left, and X, the Bob-Victoria pup, on the right:

Continued in PART 3

General info on The Sieger Show Experience with tour guide Fred Lanting 

The  SV Bundessieger-Zuchtschau (BSZS or Sieger Show) in Germany is generally held in the last week of August or first week in September at a different location each year, depending on stadiums available. (The cost of stadium for this one-weekend event, and the competition with soccer/football events that sign contracts for many per year, determine the choice.) For the past 20 years or so, I have offered my non-profit 6-7-day guided tour of the show and sightseeing, including visits to kennels and training clubs. Get an SV judge's perspective of the bloodlines and procedures, along with experienced introductions to Germany's culture and beauty. My groups come from all parts of the globe, so even just the companionship is like a world-travel experience. We usually arrive on the Wednesday or Thursday before the show, and return the following Wednesday.

Looking for a great dog-related experience combined with seeing a different part of the world? Whatever your breed or activity in dogs, the annual Lanting guided show-and-sightseeing tour could be the experience of a lifetime. Read my annual “Impressions” articles on various websites for an idea of what we've seen in recent years. Tours centered on other countries’ Sieger Shows, the BSP, and world Schutzhund trials are also available if enough people sign up.    

None of "my people" have ever been sorry, and all have wished they had done it earlier! You will see the best of the breed, meet important GSD people, sometimes see another country or two, and have the over-all greatest dog show experience of your life. I also include, if you decide to join us, a variety of travel tips. I offer an SV conformation judge's perspective of the show (I also have AKC, UKC, and foreign judging experience). One year, when a travel-agency tour leader again deserted his group, they came to where my group was sitting and asked me questions. References available from previous tour participants. Testimonials are numerous. I hope you will join us and recommend this tour to your friends and acquaintances. As a judge with much experience in Schutzhund training and competition, and being very familiar with Western Europe, I am able to give the best tour possible. People going it on their own cannot see the important parts of the country (sometimes we tour adjacent countries, too), and paying for your rental car is more than chipping in to pay for the van and my expenses. Read my "Impressions" on various websites for an idea of what we've seen in recent years.

There will be 3 long days of the big show, and about 3 to 4 days of sightseeing and visits. Please let me know as soon as you can, with a $400 (US) deposit, so I can start putting my notification list together and finalize (hold) hotel reservations for you. There is a lot of work involved in putting together such a tour! I will make the hotel plans based on your deposits, & arrange the visits and van(s). Easy, fun, educational and, for most --- the unique trip of a lifetime. You will not be any younger next year, and if you don't make the decision to get out there and smell the roses NOW, while you think of it, you're more likely than not to lose the opportunity and desire.  Join the group! Tell others about it, too. Fred 

Contact me at  Mr.GSD[at]netscape.com and tell your friends and Internet contacts.
Postal mail: 3565 Parches Cove, Union Grove, AL  35175-8422 USA

Editor’s Note:  A well-respected and frequent GSD specialty and all-breed judge for many clubs around the world, with KC and other-country credentials, Mr. Lanting since 1966 has lectured on Gait-and-Structure, Canine Orthopedic Disorders, and other topics, and has judged in about 30 countries, including the prestigious FCI Asian Shows hosted by Japan Kennel Club and the KC of India, the Scottish Kennel Club, and many National Specialties in the USA and elsewhere. He has been described by a former OFA director as the world’s leading non-veterinarian authority on hip dysplasia. A dog breeder since 1945, a GSD owner since 1947, and a show judge since 1979, he has lectured at numerous veterinary schools in the USA and abroad. He is the author of “must read” books for the dog owner (see below for ordering info).  Curriculum Vitae available upon request.

Announcing the new “Canine HD and Other Orthopedics Disorders” book: The expanded revision is a comprehensive (nearly 600-page), amply illustrated, annotated, monumental work that is suitable as a coffee-table book, a reference work for breeders and veterinarians, and a study adjunct for veterinary students. It is equally valuable for the owner of any breed. It covers every aspect of HD and other orthopedic, bone, or spinal disorders, and includes genetics, diagnostic methods, treatment options, and the role of environment. Your autographed copy will be mailed from the USA as soon as the appropriate amount is received and is processed. Pricing: US $68, plus $5 postage in the U.S., or ask about mail overseas. Combine orders with “The Total German Shepherd Dog” by the same author ($50 plus postage). 17 of the 20 chapters are suitable for owners of any breed.