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Breeding – Dogs or Pedigrees?

By Dr. Catherine Marley


All dogs carry defective genes.  These defective genes are usually “recessive” – that is, their expression can be covered up by the presence of a normal gene for that function.  It is estimated that the average dog carries 4 to 7 defective genes in it’s DNA. (The human estimate is 10 to 12).  Since genes are always carried in pairs, most of these abnormal genes are carried in a only single dose, so that their presence is completely concealed by the other, normal gene.


What is a gene?  A useful analogy is that a gene is like a set of instructions given to a particular workman doing a small job on a very big construction site.  Each workman gets two sets of plans.  If one set is damaged, he still has one good set, and the job can proceed.  But if both sets are damaged the job will not be finished, or it will be done wrong.  A gene is a large molecule, a long double strand of DNA, composed of a backbone of two long sugar molecules linked by pairs of smaller molecules called “bases” or “nucleotides”.  It is the sequence of these nucleotides that encodes the information contained in a gene.


How does a gene become defective?  During the normal cell division, an exact copy is made of each and every gene in the cell, and then it divides into two daughter cells which are each an exact copy of the original cell.  Defective genes are caused by a “mutation”.  If something happens to disrupt the exact replication of the DNA during the cell division, a defective gene results.  Only a few changes in the base sequence can render the information in that gene useless.  The process of aging is undoubtedly the effect of accumulated random defects of this sort, as are most types of cancer.


In the formation of egg and sperm, a special type of division takes place.  Instead of replicating the genetic material, so that both the daughter cells have a full complement of genes (two genes of each type), the genetic material is divided, so that each reproductive cell has only one gene of each type.  When sperm and egg finally meet, the full complement of genes is restored, and a new individual, carrying half of its mother’s genes and half of its father’s genes is created.


Selective breeding.  Nearly all breeding of domestic animals is selective as opposed to random.  Years ago, before the era of scientific genetics, breeding was done more by phenotype than by pedigree.  Race horses tended to be bred by the stopwatch.  That was where the money was.  Dairy cattle were bred by the volume and quality of their milk, meat animals, by the speed of maturation and ratio of feed to meat, and so on.  Later, it was recognized that breeding together closely related animals tended to speed up the process of “fixing” the desired traits within a few generations.


Breeding by pedigree is the type of selective breeding most often practiced today.  It nearly always involves some degree of inbreeding.  The logic is simple.  We know that an animal’s traits are genetically controlled.  We can even calculate the percentage of a particular animal’s genes residing in the cells of one of its descendants.  When we mate closely related animals whose family shows (has the phenotype of) the desired trait, we are reasonably sure it will appear in the offspring.  Some breeders have carried this practice to remarkable extremes, failing to realize there is a “catch” to the pedigree method.


What about those defective genes?  The ones you can’t see because they are “covered up” by intact ones.  When we breed closely related animals, (let us say because they have super rears), we can see the desired trait.  This trait is genetically controlled, like all traits.  These two closely related animals share the gene for their super rears as a result of their close genetic relationship.  What we can’t see is the PRA gene or the kidney disease gene that these two animals also share as a result of their close genetic relationship.  When we double up on the good rears we are also doubling up on the particular hidden defect they share.


We can see the results of this type of concentration of mutations in some human populations which have been relatively inbred by reason of isolation due to status, geography, or religion.  Some examples that come to mind are Tay-Sachs disease in eastern European Jews, and hemophilia in some royal families.


Phenotype breeding has been neglected in recent years.  It has fallen into underserved disrepute as the more popular inbreeding has produced faster and more dramatic changes.  I say undeservedly, because it has much to recommend it, and avoids some of the serious pitfalls of inbreeding.


Again, we look at phenotype of two relatively unrelated animals.  They both have good rears, which we want.  Why do they share this trait?  For the same reason that the two related ones did: they both have the set of genes which produce good rears.  But what about the hidden, bad genes?  Since these animals could not have been selected for unseen characteristics, (after all, if you can’t see it you can’t consciously select for it), they probably do not share many of these defective genes.  To be sure, they still carry their load of defects in their own private collections, but they most likely each carry a different set.  This being the case, it is unlikely that any one of their offspring will inherit two copies of the same defective gene.  It is very likely, however, that they will all have good rears.


Phenotype breeding is still selective breeding.  We are selecting those animals which show the desired traits, while minimizing the probability of doubling up on hidden, undesired ones.  Inbreeding and linebreeding, one the other hand, selects for both the phenotypic and genotypic traits, and dramatically increases the probability of producing animals homozygous for defects.


The lesson in all this is that we should pay less attention to pedigrees, particularly in terms of looking for similarities on paper when we breed, and more attention to the dogs themselves.  All too many breeders make their breeding decisions on paper, and not in the flesh.  We need to consider the pedigrees as they relate to the qualities of the parent animal – did his mom and dad have good rears – rather than to insist he be related to our prospective brood bitch.  We can get the results we want by breeding unrelated “like to like”, without the tragic by products of inbreeding.


A Glossary of Genetic Terms


Allels:  different versions of the same gene (found at the same locus but in homologous chromosomes of in different individuals) that may produce different phenotypes.


Allele frequency:  the fraction of all the alleles of a gene in a population that are of one type.


Assortative mating:  a mating scheme that relies on the pairing of unrelated individuals with similar phenotypes to obtain consistency of type and reinforce desirable traits.


Codominant alleles:  two alleles that have different effects that are distinguishable in a heterozygous individual (e.g. AB blood groups)


Cross-breeding:  crossing two different breeds


Dominant allele:  one that determines the phenotype even when there is only one copy (i.e. in a heterozygous individual)


Drift:  changes in allele frequencies over time due to chance (as opposed to selection or mutation)


Effective population size (Ne):  the size of a hypothetical stable, randomly-mating population that would have the same rate of gene loss or increase in inbreeding as the real population (size N).  As all finite populations are inbred to some degree and generally do not choose mates at random, Ne is typically 1/10N or less, particularly if fewer males breed than females.


Epistasis:  used to describe the situation where one gene’s expression prevents the expression of another (e.g. you cannot determine whether an albino would have had black or brown hair, though these two traits are controlled by separate genes.)


Fitness (relative):  The reproduction success of individuals of a particular genotype relative to the most fit genotype.


Fixation:  loss of all alleles of a gene but one


Founder:  an individual drawn from a source population who contributes genetically to the derived subpopulation.


Founder effect:  changes in allele frequencies that occur when a subpopulation is formed from a larger one.  Typically many rare and usually undesirable alleles are excluded while a few carried by the founders get a big boost in frequency.


Founder equivalents:  the number of hypothetical founders that would have the same diversity as the descendant population.  Generally much smaller than the actual number due to unequal use and allele loss (gene dropping).


Gene:  that portion of the genome that carries the information for a single protein.  (In cases of proteins with multiple subunits, there may be a gene for each.)


Gene dropping:  loss of alleles due to genetic drift


Genetic bottleneck:  when population numbers are temporarily reduced to a level insufficient to maintain the diversity in the population


Genetic diversity:  usually expressed in terms of percentage of genes that are polymorphic and/or are heterozygous.


Genome:  the total genetic makeup of an organism


Heritable:  passed on from parents to progeny through the chromosomes/DNA.


Heritability:  the fraction of the variability in a trait that is caused by genetic differences


Heterozygous:  carrying two different alleles of a gene


Heterozygous advantage:  a situation where the heterozygous genotype for a particular gene shows the highest relative fitness


Heterozygous insufficiency:  when the heterozygous genotype lacks sufficient gene product to have the normal phenotype.  (Approximately equivalent to partial dominance.)


Heterosis:  a situation where crossing two inbred lines yields progeny that are more healthy/vigorous than their parents.  (More commonly used in plant breeding.)


Homologous chromosomes:  in higher plants and animals, chromosomes are found in nearly identical “homologous” pairs, one coming from the sire and the other from the dam.  A dog has 39 pairs, or 78 in total.  Only one of each, chosen at random, is passed on through eggs or sperm to the progeny.


Linebreeding:  a scheme that attempts to maintain a high contribution of one or two ancestors through successive generations.  Often used by breeders for any inbreeding less intensive than between first-degree relatives.


Linkage:  a measure of how frequently two genes found on the same chromosome remain together during gamete (egg or sperm) formation.


Locus:  the location of a gene on a chromosome.


Map (aka linage map):  a drawing showing the location of and relative distances between genes on a chromosome.


Mean kinship (mk):  a measure of how related an individual is to the other members of a population.  Generally computed as the average IC for the hypothetical progeny of the individual mated to all other members of the population (both sexes).  A low average mk for a population indicates that most of the diversity carried by the founders has been retained.


Monomorphic genes:  have only one common allele (rare alleles with frequencies of less than 0.001% may still occur).


Mutation:  a change in the sequence of the base pairs in a DNA molecule.


Mutation rate:  the number of new mutations that occur per gene per gamete per generation.


Outcrossing:  mating two individuals of the same breed that are sufficiently unrelated that the IC of the progeny is lower than the average of the parents.


Polymorphic genes:  have 2 or more common alleles in the population


Recombination:  the reciprocal exchange of portions of two homologous chromosomes (usually equivalent) during gamete formation.


Recombinant frequency (RF):  how often two linked genes are separated by recombination, generally expressed as a percentage of total progeny.