The Ins and Outs of Pedigree Analysis, Genetic Diversity, and Genetic Disease Control

by Jerold S. Bell, D.V.M.

(This is an updated version of an article that originally appeared in the American Kennel Club Gazette in September 1992 entitled, “Getting What You Want From Your Breeding Program.” It is reprinted with the permission of Dr. Bell.)

IT’S ALL IN THE GENES

As dog breeders, we engage in genetic "experiments" each time we plan a mating. The type of mating selected should coincide with your goals. To some breeders, determining which traits will appear in the offspring of a mating is like rolling the dice ‑ a combination of luck and chance. For others, producing certain traits involves more skill than luck ‑ the result of careful study and planning. As breeders, we must understand how we manipulate genes within our breeding stock to produce the kinds of dogs we want. We have to first understand dogs as a species, then dogs as genetic individuals.

The species, Canis familiaris, includes all breeds of the domestic dog. Although we can argue that there is little similarity between a Chihuahua and a Saint Bernard, or that established breeds are separate entities among themselves, they all are genetically the same species. While a mating within a breed may be considered outbred, it still must be viewed as part of the whole genetic picture: a mating within an isolated, closely related, interbred population. Each breed was developed by close breeding and inbreeding among a small group of founding canine ancestors, either through a long period of genetic selection or by intensely inbreeding a smaller number of generations. The process established the breed's characteristics and made the dogs in it breed true.

When evaluating your breeding program, remember that most traits you're seeking cannot be changed, fixed or created in a single generation. The more information you can obtain on how certain traits have been transmitted by your dog's ancestors, the better you can prioritize your breeding goals. Tens of thousands of genes interact to produce a single dog. All genes are inherited in pairs, one pair from the father and one from the mother. If the pair of inherited genes from both parents is identical, the pair is called homozygous. If the genes in the pair are not alike, the pair is called heterozygous. Fortunately, the gene pairs that make a dog a dog and not a cat are always homozygous. Similarly, the gene pairs that make a certain breed always breed true are also homozygous. . Therefore, a large proportion of homozygous non-variable pairs - those that give a breed its specific standard - exist within each breed. It is the variable gene pairs, like those that control color, size and angulation, which produce variations within a breed.

BREEDING BY PEDIGREE

Outbreeding brings together two dogs less related than the average for the breed. This promotes more heterozygosity, and gene diversity within each dog by matching pairs of unrelated genes from different ancestors. Outbreeding can also mask the expression of recessive genes, and allow their propagation in the carrier state.

Most outbreeding tends to produce more variation within a litter. An exception would be if the parents are so dissimilar that they create a uniformity of heterozygosity. This is what usually occurs in a mismating between two breeds. The resultant litter tends to be uniform, but demonstrates "half‑way points" between the dissimilar traits of the parents. Such litters may be phenotypically uniform, but will rarely breed true due to the mix of dissimilar genes.

A reason to outbreed would be to bring in new traits that your breeding stock does not possess. While the parents may be genetically dissimilar, you should choose a mate that corrects your dog's faults but phenotypically complements your dog's good traits.

It is not unusual to produce an excellent quality dog from an outbred litter. The abundance of genetic variability can place all the right pieces in one individual. Many top‑winning show dogs are outbred. Consequently, however, they may have low inbreeding coefficients and may lack the ability to uniformly pass on their good traits to their offspring. After an outbreeding, breeders may want to breed back to dogs related to their original stock, to increase homozygosity and attempt to solidify newly acquired traits.

Linebreeding attempts to concentrate the genes of a specific ancestor or ancestors through their appearance multiple times in a pedigree. The ancestor should appear behind more than one offspring. If an ancestor always appears behind the same offspring, you are only linebreeding on the approximately 50 percent of the genes passed to the offspring and not the ancestor itself.

It is better for linebred ancestors to appear on both the sire's and the dam's sides of the pedigree. That way their genes have a better chance of pairing back up in the resultant pups. Genes from common ancestors have a greater chance of expression when paired with each other than when paired with genes from other individuals, which may mask or alter their effects.

A linebreeding may produce a puppy with magnificent qualities, but if those qualities are not present in any of the ancestors the pup has been linebred on, it may not breed true. Therefore, careful selection of mates is important, but careful selection of puppies from the resultant litter is also important to fulfill your genetic goals. Without this, you are reducing your chances of concentrating the genes of the linebred ancestor.

Increasing an individual's homozygosity through linebreeding may not, however, reproduce an outbred ancestor. If an ancestor is outbred and generally heterozygous (Aa), increasing homozygosity will produce more AA and aa. The way to reproduce an outbred ancestor is to mate two individuals that mimic the appearance and pedigree of the ancestor's parents.

Inbreeding significantly increases homozygosity, and therefore uniformity in litters. Inbreeding can increase the expression of both beneficial and detrimental recessive genes through pairing up. If a recessive gene (a) is rare in the population, it will almost always be masked by a dominant gene (A). Through inbreeding, a rare recessive gene (a) can be passed from a heterozygous (Aa) common ancestor through both the sire and dam, creating a homozygous recessive (aa) offspring. Inbreeding does not create undesirable genes, it simply increases the expression of those that are already present in a heterozygous state.

Inbreeding can exacerbate a tendency toward disorders controlled by multiple genes, such as hip dysplasia and congenital heart anomalies. Unless you have prior knowledge of what milder linebreedings on the common ancestors have produced, inbreeding may expose your puppies (and puppy buyers) to extraordinary risk of genetic defects. Research has shown that inbreeding depression, or diminished health and viability through inbreeding is directly related to the amount of detrimental recessive genes present. Some lines thrive with inbreeding, and some do not.

PEDIGREE ANALYSIS

Geneticists' and breeders' definitions of inbreeding vary. A geneticist views inbreeding as a measurable number that goes up whenever there is a common ancestor between the sire's and dam's sides of the pedigree; a breeder considers inbreeding to be close inbreeding, such as father‑to‑daughter or brother‑to‑sister matings. A common ancestor, even in the eighth generation, will increase the measurable amount of inbreeding in the pedigree.

The inbreeding coefficient (or Wright’s coefficient) is an estimate of the percentage of all the variable gene pairs that are homozygous due to inheritance from common ancestors. It is also the average chance that any single gene pair is homozygous due to inheritance from a common ancestor. In order to determine whether a particular mating is an outbreeding or inbreeding relative to your breed, you must determine the breed's average inbreeding coefficient. The average inbreeding coefficient of a breed will vary depending on the breed's popularity or the age of its breeding population. A mating with an inbreeding coefficient of 14 percent based on a ten generation pedigree, would be considered moderate inbreeding for a Labrador Retriever (a popular breed with a low average inbreeding coefficient), but would be considered outbred for an Irish Water Spaniel (a rare breed with a higher average inbreeding coefficient).

For the calculated inbreeding coefficient of a pedigree to be accurate, it must be based on several generations. Inbreeding in the fifth and later generations (background inbreeding) often has a profound effect on the genetic makeup of the offspring represented by the pedigree. In studies conducted on dog breeds, the difference in inbreeding coefficients based on four versus eight generation pedigrees varied immensely. A four generation pedigree containing 28 unique ancestors for 30 positions in the pedigree could generate a low inbreeding coefficient, while eight generations of the same pedigree, which contained 212 unique ancestors out of 510 possible positions, had a considerably higher inbreeding coefficient. What seemed like an outbred mix of genes in a couple of generations, appeared as a linebred concentration of genes from influential ancestors in extended generations.

The process of calculating coefficients is too complex to present here. Several books that include how to compute coefficients are indicated at the end of this article; some computerized canine pedigree programs also compute coefficients. The analyses in this article were performed using CompuPed, by RCI Software.

Pedigree of Gordon Setter Laurel Hill Braxfield Bilye

( a spayed female owned by Dr. Jerold and Mrs. Candice Bell, and co-bred by Mary Poos and Laura Bedford.)

Dual CH Loch Adair Monarch

CH Sutherland MacDuff

| CH Sutherland Dunnideer Waltz

CH Sutherland Gallant

| | CH Afternod Kyle of Sutherland

| CH Sutherland Pavane

| CH Sutherland Xenia

CH Loch Adair Foxfire

| | Afternod Fidemac

| | CH Loch Adair Peer of Sutherland, CD

| | | CH Wee Laurie Adair

| CH Sutherland Lass of Shambray

| | CH Afternod Callant

| CH Afternod Karma

| CH Afternod Amber

CH Braxfield Andrew of Aberdeen

| | Afternod Fidemac

| | Am.Cn.CH Afternod Scot of Blackbay, CD

| | | CH Afternod Alder

| | Am.Cn.CH Forecast Trade Winds, CD

| | | | Bud O'Field Brookview

| | | CH Oak Lynn's Bonnie Bridget

| | | Borderland Taupie

| CH Afternod Ember VI, CD

| | CH Afternod Simon

| | Afternod Profile of Sark

| | | CH Afternod Heiress of Sark

| CH Afternod Ember V

| | CH Afternod Callant

| CH Afternod Maud MacKenzie

| CH Afternod Amber

LAUREL HILL BRAXFIELD BILYE

| CH Afternod Callant

| Dual CH Loch Adair Monarch

| | Loch Adair Diana of Redchico

| CH Sutherland MacDuff

| | | CH Afternod Anagram

| | CH Sutherland Dunnideer Waltz

| | CH Hi‑Laway's Calopin

| CH Kendelee Pendragon

| | | CH Afternod Callant

| | | CH Wee Jock Adair, CD

| | | | Loch Adair Diana of Redchico

| | CH Afternod Nighean Kendelee

| | | CH Afternod Simon

| | CH Afternod Wendee

| | Afternod Dee of Aberdeen

CH Halcyon Belle‑Amie

| Dual CH Loch Adair Monarch

| CH Sutherland MacDuff

| | CH Sutherland Dunnideer Waltz

| CH Sutherland Gallant

| | | CH Afternod Kyle of Sutherland

| | CH Sutherland Pavane

| | CH Sutherland Xenia

CH Loch Adair Firefly, WD

| Afternod Fidemac

| CH Loch Adair Peer of Sutherland, CD

| | CH Wee Laurie Adair

CH Sutherland Lass of Shambray

| CH Afternod Callant

CH Afternod Karma

CH Afternod Amber

To visualize some of these concepts, please refer to the above pedigree. Linebred ancestors in this pedigree are in color, to help visualize their contribution. The paternal grandsire, CH Loch Adair Foxfire, and the maternal grandam, CH Loch Adair Firefly WD, are full siblings, making this a first‑cousin mating. The inbreeding coefficient for a first cousin mating is 6.25%, which is considered a mild level of inbreeding. Lists of inbreeding coefficients based on different types of matings are shown in the accompanying table.

In Bilye’s pedigree, an inbreeding coefficient based on four generations computes to 7.81%. This is not significantly different from the estimate based on the first‑cousin mating alone. Inbreeding coefficients based on increasing numbers of generations are as follows: five generations, 13.34%; six generations, 18.19%; seven generations, 22.78%; eight generations, 24.01%; ten generations, 28.63%; and twelve generations, 30.81%. The inbreeding coefficient of 30.81 percent is more than what you would find in a parent‑to‑offspring mating (25%). As you can see, the background inbreeding has far more influence on the total inbreeding coefficient than the first‑cousin mating, which only appears to be its strongest influence.

Knowledge of the degree of inbreeding in a pedigree does not necessarily help you unless you know whose genes are being concentrated. The percent blood coefficient measures the relatedness between an ancestor and the individual represented by the pedigree. It estimates the probable percentage of genes passed down from a common ancestor. We know that a parent passes on an average of 50% of its genes, while a grandparent passes on 25%, a great‑grandparent 12.5%, and so on. For every time the ancestor appears in the pedigree, its percentage of passed‑on genes can be added up and its "percentage of blood" estimated.

In many breeds, an influential individual may not appear until later generations, but then will appear so many times that it necessarily contributes a large proportion of genes to the pedigree. This can occur in breeds, due either prolific ancestors (usually stud dogs), or a small population of dogs originating the breed. Based on a twenty-five generation pedigree of Bilye, there are only 852 unique ancestors who appear a total of over twenty-million times.

Pedigree Analysis of Laurel Hill Braxfield Bilye

(computed to 25 generations)

1st Generation Linebred Ancestors	Percentage of Blood	Of Appearance in Pedigree	Number Times in Pedigree
CH Afternod Drambuie	33.20%	6	33
CH Afternod Sue	27.05%	7	61
CH Afternod Callant	26.56%	5	13
Grand-Parents	25.00%	2	1
CH Sutherland Gallant	25.00%	3	2
CH Sutherland MacDuff	25.00%	3	3
CH Sutherland Lass of Shambray	25.00%	3	2
CH Wilson's Corrie, C.D.	22.30%	7	200
CH Afternod Buchanon	20.22%	7	48
Loch Adair Diana of Redchico	17.97%	5	12
CH EEGs Scotia Nodrog Rettes	17.76%	8	181
Afternod Ember of Gordon Hill	17.14%	8	76
CH Afternod Hickory	16.21%	6	27
CH Black Rogue of Serlway	15.72%	9	480
CH Afternod Woodbine	14.45%	6	15
CH Fasts Falcon of Windy Hill	13.82%	8	66
Afternod Fidemac	13.67%	5	7
CH Page's MacDonegal II	13.43%	7	56
Afternod Hedera	13.38%	7	56
CH Downside Bonnie of Serlway	12.90%	10	708
Peter of Crombie	12.76%	11	3,887
Great-Grand-Parents	12.50%	3	1
CH Afternod Amber	12.50%