The most unfortunate result of a base-pair substitution is when
this mutation codes for a stop codon. A codon is that portion of
the messenger RNA that codes for a specific amino acid. A start
codon (AUG) serves rather like a capital letter indicating the start
of a sentence. A stop codon is a codon that does not specify an
amino acid, and serves much as a comma or a period punctuating
the genetic message. The Genetic Code is composed of sixty-four
different arrangements of three nucleotides each (codons). This
set of combinations codes for a total of twenty different amino
acids and the stop codon. Some of the combinations code for
the same amino acid and three of them signal for termination.

This redundancy is why some base-pair substitutions have no
effect, because the change results in the same amino acid being
produced. If, by chance, a mutation produces one of the stop
codons, than the process of making the protein is terminated.
This is not good.

"An example of this type of mutation is the one that leads to a
form of progressive retinal atrophy (PRA) in the Irish setter. A
substitution of an A for a G produces the stop codon (TAG)
that replaces the normal codon for the amino acid tryptophan
(TGG). This prevents a protein called PDEB (phosphodiesterase
beta) from being produced in its full length form. The shortened
protein is unstable and is degraded by the retinal cells in which
it is needed. The lack of this protein causes the retina to
degenerate, resulting in blindness in those Irish setters that
have two copies of the mutant gene, and no normal copy."
.
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Frameshift Mutations
.
In the normal cell replication process, DNA is transcribed into
messenger RNA, which in turn is translated into a series of
amino acids. This always occurs in a specific manner, i.e., it
always begins at a definite spot and it is 'read' in multiples
of three (codon) and in a particular orientation along the length
of the strand of DNA . This is called a reading frame. If there
is an addition or deletion of one or two base-pairs, then the
result is often a very altered sequence of amino acids in the
final protein product. This is definitly not good.
.
"An example of this is the mutation that leads to an inherited
form of anemia in Basenjis. A deletion of a single nucleotide
in the 433rd codon of the gene encoding a protein called PK
(pyruvate kinase) causes a shift in the reading frame. The
misformed and shortened protein (a new stop
.
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Splice-site mutations
.
Molecular geneticists used to think that all of the DNA coding
for a particular protein was continuous, that is, until they
started to look at more complex organisims. What they found,
in these types of cells, is that the DNA that makes up a gene
is often distributed in discontinuous sections called exons,
interspersed with long segments of non-coding DNA known
as introns. These sections are transcribed into messenger RNA
along with the exons, but before the RNA is translated into a
protein they are 'edited' or 'spliced' out. A change of even a
single nucleotide in one of the exons of the gene can cause
a shift or alteration of the splice-site.
.
A genetic disease that affects Dobermans is a perfect illustration
of this type of mutation. Von Willebrand disease is a bleeding
disorder that effects the animals ability to form blood clots.
Other breeds also have this disease, but what had perplexed
those doing vWD research , was that Dobermans appeared
to have a milder form of the disease. The discovery of a
splice-site mutation that codes for von Willebrand factor has
cleared up their mystery. George Brewer MD of the University
of Michigan suggests that one use the following analogy in
order to explain how the mutation functions.
.
Imagine that a freight train is supposed to go from point A to
point B along a railroad track. Somewhere between A and B is
a spot where a sidetrack goes to point C. Normally, the train
never goes to point C because the switch, that connects the
two tracks, is never thrown. Then the switch is broken (the
mutation) and the lock that prevents the track from connecting
to point C is no longer effective. The switch can now toggle
back and forth, sending some trains to point B and sometimes
to point C. In affected Dobermans, the defective switch sends
the train to the wrong destination and about 95% of the time,
the train rumbles over the cliff and is never heard from again.
(and the proper protein is never made) However, sometimes
the switch jiggles the right way and the train ends up at the
normal destination and the proper protein is made.
.
If both copies of the gene are mutated, then each gene can
make the right protein about 5 to 10% of the time. Affected
.
Dobermans are thus producing von Willebrand factor
.
.
Diversity and Recombination
.
In mammals, DNA is not just one continuous strand, but exists
within the cell nucleus in a number of pieces of genetic material
called chromatin. Before a cell divides, the chromatin collects
itself up into a structure called chromosomes. Dogs have a total
of 78 chromosomes, humans have 46. The total number of
chromosomes is called the diploid or 2n number. The point of
this division is so one member of each chromosome pair can
become part of a gamete, or sex cell (egg and sperm). These
gametes have half the number of total chromosomes (termed
haploid, or n), so when they join together the resulting progeny
will be 2n. The sire contributes 39 chromosomes and the dam
another 39. They form into matching (homologous) pairs that
have the same type of genes on them, but not necessarily in
the same form. For instance, the gene that codes for albinism
exists at the same position, on the same chromosome, in both
parents.
.
However, one parent has the gene that produces pigmentation
and the other carries the gene that produces no pigmentation.
The same gene in a different form is called an allele. If the
genes are of the same form then the dog is homozygous at
that position. If the animal has different alleles at a certain
location, then it is said to be heterozygous. In a diverse
population, almost every gene has multiple forms of the same
gene. This is known as genetic diversity. Another genetic
process, called recombination, further adds to genetic diversity.
This is how it works.
.
Prior to division a cell duplicates its DNA and in the process
four chromosomes are produced: two sets of homologous
(matching) pairs. Before the cell divides these homologous
pairs line up and sometimes they swap DNA. This DNA
swapping process is called recombination. If the original
pair was heterozygous (not matching) at two genes, say
A and A+ and B and B+, then the possible gametes formed
would be AB, A+B+. A B+, and A+ B. Without recombination,
if the A allele was on the same chromosome as the B allele,
they would always be inherited together. In fact, such "linked"
chromosomes more often than not are inherited together,
because the chances of such a split and subsequent
recombination decreases the less space there is between the
two genes. When recombination does occur, [Susan, I think
we must have some graphics here?otherwise no one is going
to get it( JCC)?agreed (DCC)] two gametes would be parental
types and two of them would be a combination of their
parents. Without recombination, traits carried by genes on
one chromosome would always be inherited as a group,
and dogs would basically only have 39 different "gene-groups."
.
The take home message should be that recombination adds
to the genetic diversity. This is especially important in a highly
in-bred population, such as a specific dog breed.
.
.
Do breeders want genetic diversity?
.
Dog breeders do NOT want genetic diversity, except in certain
breeds in which function is still considered the number one
priority. For most breeds they want to fix "TYPE", type being
the phenotype or how the dog looks as opposed to genotype,
the genetic makeup of the dog. In order to produce type, dog
breeders have produced a highly in-bred animal with multiple
genes that are homozygous for those traits that specify their
breed.
.
Unfortunately, along with introducing and refining those
traits, a plethora of deleterious genes came along for the
ride. Our job now, as breeders is to somehow retain those
genes that express our breed's type and yet remove those
that cause disease and genetically transmitted defects.
Before we can really explore how a particular trait is
transmitted or lost within a closed breeding group we will
need to introduce and explain such concepts as founder
effect, inbreeding depression and linkage disequilibrium.
What is briefly introduced here and expanded on in the
second article will be a short course in Population Genetics,
the technical name for what happens to the gene pool
from which reproductive selections will be made.
.
.
What Happens When We Lose Diversity?
.
One of the purported purposes of breeding purebred dogs
is to not only improve the breeder's own stock, but to
ultimately improve the breed. The degree to which one
breeder can influence the genetic direction of a breed is
influenced by many factors; one of the most important is
the size and diversity of the existing breed population. In
the long scheme of things, individual dogs will live and die,
but if bred, their genes will live on through their progeny.
Thus from an evolutionary viewpoint, a population, or
breed, can be thought of as consisting of as the total
number of alleles, rather than individuals, present at
one time.
.
This "gene pool" is equal in size to approximately twice the
number of dogs in a population, because each dog carries
two alleles per gene (except in the case of sex-linked genes).
Evolution results when the relative proportions of alleles
change with successive populations. The more variability
that exists at one locus, the more room exists for evolutionary
change. Goals of purebred dog breeders involve increasing,
reducing, and preserving various gene frequencies within a
population.
.
Although individual dogs making up the population change,
total gene frequencies within the populations remain fairly
constant unless four specific situations (mutation, migration,
genetic drift, and non-random selection) apply. Mutation
provides the foundation of genetic variability, but without
the remaining three situations a single mutant allele will
seldom become fixed in a population. Migration refers to
the introduction of new alleles from another population,
and was especially influential in early development of breeds
through cross-breeding. Selection is the main tool of the
breeder, who chooses which dogs will pass on their genes
to the next population. Selection, plus drift, both play a
part in the phenomena known as founder effect and inbreeding
depression.
.
.
Founder Effect
.
When a new population is established by a sample (founders)
drawn from the parent population, as in the development
of a new breed, the genetic make-up of the foundation
stock will most likely be very different (simply by chance)
from that of the original population from which it was drawn.
The smaller the sample the greater the probability of
difference in that the sample does not fairly represent the
parent population. The genome of such a subpopulation
with its limited number of founder individuals will carry the
alleles of the new group rather than those of the source
group. An allele that is quite rare normally in the original
population might be very common is the new one, and visa
a versa. This, in effect, abruptly changes the kinds of alleles
represented and how often they appear. This founder effect
is in essence a form of acute genetic drift (variation in gene
frequency from one generation to another due to chance).
The problem with losing genetic diversity is severalfold. Once
lost, an allele cannot reenter the population except through
mutation (unlikely) or migration (which, if a breed is
considered a population, means either going back to its
rootstock from its country of origin or crossing with another
breed). Genetic diversity is the foundation of evolution; it
may be acceptable to loose deleterious alleles due to selection,
but the loss of other unknown alleles due to chance reduces
the variability upon which selection can act, and thus the
possibility of further evolution. Loss of genetic diversity also
can result in inbreeding depression.
.
.
Inbreeding and Inbreeding Depression:
You can't fool Mother Nature.
.
Evolution is thought to be a gradual change in the kind and
frequencies of alleles. Those mutants that are harmful are
either eliminated or kept at low frequencies by natural selection.
However; with artificial selection , especially when a breed is
being developed, it is the individuals that exhibit the greatest
expression of the desired traits that are chosen to breed the
subsequent generations. When only a few dogs are used to
produce the next generation, a high proportion of their genes
will be in the next population of potential breeding animals.
When these related dogs are then interbred, the chances of
them passing on the same allele that they both received from
their sire and dam is 25%. Thus, inbreeding increases the
chance that subsequent offspring will carry identical copies
of the same allele (be homozygous at that locus). Increasing
inbreeding increases the chance of homozygosity and can lead
to the loss of one of the alleles from the population.
.
Breeders walk a tightrope between needing to reduce genetic
variation to maintain uniform breed type and needing to
maintain genetic diversity to avoid inbreeding depression, which
results from homozygosity of deleterious alleles. The majority
of alleles detrimental to life and reproduction tend to be recessive,
for the simple reason that if they were dominant, they would
have been expressed in the individual's phenotype, and that
individual would have been less likely to reproduce. If recessive,
only those individuals with homozygous recessive alleles would
be reproductively compromised; heterozygotes would be
unaffected. Every dog (and every human) carries deleterious
recessive alleles, so the chances of the foundation stock carrying
them is virtually 100%. If very few dogs were used as
foundation stock, their progeny would have to be interbred, and
in only a few generations all of the dogs would be closely
related. Breeding closely related dogs is inbreeding. An inbred
dog has a greater likelihood of receiving the same allele from
both its sire and dam, and thus a greater likelihood of being
homozygous for a deleterious trait. In an inbred population,
as long as the animals can still reproduce, this homozygosity
can become fixed in the population due to the chance loss
of the other allele. What this means for the breeder is that too
great a reliance on inbreeding will lead to loss of 'fitness', i.e.,
failure to reproduce. Fewer litters are produced, the number of
whelps will decrease and those that are born will fail to thrive.
Taken to extreme, the effective breeding population could be
so diminished that the breed would face extinction.
.
.
Bottleneck
.
Modern dog breeds have all been subjected to a founder effect,
and many of them have had their gene pools further reduced
by subsequent genetic bottlenecks. The best-documented case
of a canine bottleneck was created by World War II, when
hardships in Europe made it impossible to keep many dogs,
especially giant ones. The populations of giant breeds in
Europe were practically decimated after the war, and some
breeds had to rely upon only a few survivors or imports from
less affected areas?in effect, reducing the gene pool and
creating a second, even more limited, foundation for the breed.
.
Other bottlenecks are created when a breed, for whatever
reason, becomes extremely unpopular and rare, or when dogs
from one country (or worse, one kennel) are used to found
the breed in a new part of the world. Yet one of the most
pervasive bottlenecks is brought on voluntarily by breeders:
the rush to breed to only a few favored sires, the 'flavor of
the month', while the majority of potential breeding males
are never bred.
.
This bottleneck is made all the worse by the fact that the
majority of breeding bitches are often sired by a handful
of the last generation's "favored sons". In fact, the effective
population size can never be greater than four times the
number of males in a population, no matter how many
breeding females exist . In certain rare breeds, their effective
breeding population is thus so reduced, that they are in
effect, in a genetic cul-de-sac.
.
.
Conclusion
.
We have considered the origin of the dog, how it evolved
from precursors and how initially there was tremendous
genetic diversity within the species. We then examined how
mutations occur and contribute to that diversity. It was
then necessary to introduce those factors that reduce diversity
when new dog breeds are established, such as founder
effect and inbreeding. Our goal was to inform breeders of
the dangers inherent in common breeding practices that
can exacerbate the problems to the point that viability is lost.
.
In Part II of this series, we will continue our discussion of
some of the concepts involved with population genetics
and suggest ways for preventing or correcting the problems
associated with highly inbred populations. We will also
introduce and clarify such molecular genetic terms as dominant,
recessive, and co-dominant traits which are central and
fundamental to the breeding selection process.
.
So fundamental are these concepts that no breeder can
honestly claim to be an ethical breeder without a working
understanding of the underlying principles. At a still higher
level of complexity, but still of extreme importance to
breeders in their selections for breeding, we will need to
deal with such ideas as penetrance, overdominance and
best of all, epistasis. This may seem a little daunting at
first, but the health and future of our favorite companion
may depend upon what we breeders do now...so hang on
tight, as its apt to be a wild ride.
.
.
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