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Canine Genetics
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Canine Genetics
« on: May 01, 2013, 02:13:43 AM »


As I have become more involved with “breeders” in the canine world I have come to realize there is a substantial need for knowledge on the fundamentals of genetics and heredity.  What will be discussed here has long been accepted as factual and fundamental…and has been developed by the study of genetics in scientifically controlled breeding populations.  It is not speculation, but is based upon years of research from actual experiments and thousands of tests from both within the lab and within the field.  This report will largely be based on the fundamentals of gamete formation and recombination.  This report is just meant to provide a simple understanding of the fundamentals of genetics and should not be used exclusively to determine breeding pairs; however, understanding these fundamentals should help enable one to obtain their breeding goals.  A common goal in developing lines or “breeds” of dogs is consistency.  The desire for consistency has lead to a large number of breeders to use line breeding and inbreeding, but those that don’t understand what is going on at a genetic level should not use such breeding methods. Line breeding and inbreeding has its place within a breeding program when used properly. Unfortunately, many breeders fix genetics disorders within a gene pool or line as a result of inappropriately using these tactics due to a lack of understanding of the basics of genetics. This is why inbreeding is illegal among human populations. My purpose for writing this report is to enable breeders that wish to learn the fundamentals of genetics to do so…therefore, enabling them with their decision making of when to use the different types of breeding approaches (out-crossing, line-breeding, or inbreeding) within their breeding program.
 
Before we begin discussing how gamete formation and recombination occurs, lets go over a few terms…
 
Genetics – the study of heredity.
 
Heredity – the passing of traits (characteristics) from parent to offspring.  Genetic heredity is based on genetics from the inheritance of alleles.
 
Gamete – a sex cell (sperm in males and eggs in females)
 
Sperm – a male gamete
 
Egg – a female gamete
 
Zygote – a fertilized egg.  This includes the genetic information from the egg and sperm combined into one cell.
 
DNA – deoxyribonucleic acid.  Basically these are 4 nucleotides (ATGC) that make up the alleles and genetic codes within the genome (the instructions) of an organism.
 
Chromosome – a thread like structure that is formed in mitosis and meiosis that contains the DNA.
 
Genome – The entire genetic code of an organism’s DNA.  There are tens of thousands (20,000-30,000+) of loci within a genome.
 
Loci – the location of a trait within the genome is referred to as a trait’s loci.
 
Monogenic trait - a trait that is controlled by a single loci.
 
Polygenic trait - a trait that is influenced by more than one loci.
 
Trait – in this report, this term will distinguish a characteristic that may be passed from parent to offspring. Many people get trait mistaken with loci. The alternate forms of a trait are referred to as alleles. For example…such as “coat color.”  Within our example "coat color" would be the trait, while red, black, white, etc would be the allele possibilities of this trait.
 
Allele – the alternative forms of a trait.
 
Genotype – The genetic code (the combination of alleles) for a given trait.
 
Phenotype – The trait that is expressed for a given trait.
 
Homozygous – Homo means the same.  Zygous refers to the zygote (a fertilized egg where the sperm’s and egg’s contributions for a trait are the same).  Therefore, “homozygous” refers to the alleles for a given trait (the genotype) within the zygote being the same.
 
Heterozygous – Hetero means different.  Zygous refers to the zygote.  “Heterozygous” refers to the alleles for a given trait (the genotype) within the zygote being the different.
 
Meiosis – Cell division in which gametes are formed from stem cells within the ovaries or testis.  Meiosis is responsible for producing the different combinations of gametes a parent is capable of producing.
 
Mitosis – normal cell division in which daughter cells are identical to the parent cells.  This type of cell division is the driving force for growth by cell reproduction and not species reproduction.
 
Humans have 23 pairs (46 total) of homologous chromosomes.  The entire set of chromosomal pairs is known as the genome.  In canines, the number of chromosomal pairs is 39. Think of these "pairs" as being analogous to one right shoe (a father's chromosome) pairing up with one left shoe (a mother's chromosome) to make one pair of shoes (a homologous pair of chromosomes). Dogs have 39 pairs of homologous chromosomes, creating a diploid total of 78 chromosomes in all. Of these 78 chromosomes, 39 (one set) came from the mother and each chromosome pairs up with its partner homologous chromosome obtained from the father.  The picture above reveals this pairing and is called a karyotype.

The alleles that control the various traits are assigned to specific loci (addresses) within the genome. Each chromosome is so precisely arranged with its pair that the alleles for each loci from each parent line up side by side with those from the other parent. Some traits are “simple” and only have one loci. These traits are referred to as “monogenic” traits. Some traits are “complex” and are influenced by many loci (quantitative traits or polygenic traits). For every trait, each parent donates one allele at each loci. I will come back to this later in more detail.
 
Upon fertilization (the point at which a single sperm unites with the egg), the newly formed zygote now contains one allele from each parent for each loci within the entire genome (excluding the sex chromosomes).  Therefore, every organism has 2 alleles per loci, 1 from the mother + 1 from the father.  Both parents are equally responsible for an offspring’s genotype, except for the sex chromosomes (and the mitochondrial DNA, which comes from the mother). The female “X” chromosome that comes from the mother does contain a small portion of information (relatively few traits in relative terms) not found on the “Y” chromosome. Because sex-linked traits are not something we generally hear about in dogs, I will not go into great detail of sex-linked traits at this time but I will briefly mention if a trait is sex linked (found on the X chromosome and not found on the Y chromosome), the expression of an allele is determined by its sole presence on the X chromosome. For traits found in this region of the X chromosome, only one allele will determine the expression of a trait, while all other traits (those found in shared areas of the X/Y Chromosomes or on any of the other sex chromosomes), two alleles (or more for quantitative traits) are needed to determine the expression of a trait. Mitochondrial DNA is passed down to offspring via the mother, and it has been suggested that maternal mitochondrial DNA may play some role in the metabolism of the offspring.
 
As mentioned earlier, some traits are simple and controlled by a single loci.  These monogenic traits are easy to work with and begin to understand, but the polygenic traits (quantitative traits), are much more complex and offer an array of phenotypes making things much more difficult and time consuming to understand as there are many influential genes.  Just as weight is clearly influenced by a genetic predisposition for height, thickness, muscle mass, fat content, bone density, etc, there are traits that are influenced by alleles at many loci.  As a result, polygenic traits tend to be exceedingly much more difficult to select for and may require many generations of very knowledgeable and selective breeding to even begin making progress towards a specific goal.
 
Most breeders tend to understand the basic concept of dominance and recessive, but many breeders don’t realize not all genes are so simply defined. As mentioned earlier…for each loci, there is a single allele from each parent that is paired up with a single allele from the other parent.  Depending on the trait, some alleles (alternate forms of a trait) may be dominant, recessive, co-dominant, or incompletely dominant to a paired allele.  It isn’t always a complete dominance in which one dominant allele suppresses a recessive allele.
 
If complete dominance is found for the trait of interest, then the offspring only needs one allele within the genotype for the desired phenotype.  If the desired form of a trait is recessive, then the offspring needs to have a homozygous recessive genotype. In the heterozygous allelic combination is obtained in traits defined by dominance/recessive traits the phenotypic outcome of such an individual is no different than is seen in a homozygous dominant individual. However, when a trait is defined by co-dominant or incompletely dominant alleles and a heterozygous combination, the outcome will be blending of the two phenotypes. For example…lets say we are working with the color of an organism and for this trait (color gene) we define the alleles (the alternate forms) as black or white. In all cases of homozygous combinations the color will be pure, but when we obtain heterozygous individuals the outcomes will vary based upon how the traits are defined (complete dominance=only one color is expressed as it dominates the other option completely; incomplete dominance=blending of the two forms in a gray like shade; co-dominance=striped like a zebra).  This becomes more complicated if a trait is also quantitative.
 
See below for a over simplified diagram (concern of only one trait at a time) of basic genetics…
 
Assuming a trait is completely dominant and desired (the desired trait dominates the recessive trait) and controlled by a single loci…
 
F = allele designated for the favorable trait (which we will assign as dominant in this case for illustration purposes)
 
f = allele designated for the undesired trait
 
1st generation cross…(assuming you don’t breed to any undesired phenotypes)
 
In our example, we are given a father that is homozygous for the favorable trait = FF (meaning he inherited an F from his mother and an F from his father)
 
In our example, we are given a mother that is heterozygous for the favorable trait = Ff (meaning she inherited an F from one of her parents but an f from the other parent)
 
FF x Ff…when mating these two they both will select one of their alleles to donate to the
offspring creating offspring that are influenced 50% by each parent.  This can produce only 2 outcomes…Regardless of which F the father donates, because he is homozygous his donation is the same…but the mother was heterozygous; therefore, the offspring will be FF (if the mother donates a F) or Ff (if the mother donates a f).
 
A test cross is possible to determine if an individual was homozygous (FF) or heterozygous (Ff) within its genotype if the trait is controlled by complete dominance.  To do this would require breeding to an unfavorable recessive phenotype (ff).  If your selected specimen for the desired trait was homozygous then crossing FF to ff would produce 100% offspring of Ff and although all would carry the unfavored trait none would express it.  If you do this it would be best to require these animals to go to pet homes with a spay or neuter contract since all would be carriers.  If your selected specimen was heterozygous (Ff) then breeding to a homozygous recessive (ff) would cause 50% to be Ff (carriers) and the other 50% to be ff and actually display the undesired trait.  The cost of doing a test cross is it produces an entire litter of culls to determine if the desired parent was a carrier or not even though they did not express the trait.  Carriers can live fine but should not be bred hap hazardously.
 
A question of concern however is although it is clear you can select for a given trait, what is happening to the other traits in the mean time…for tens of thousands of loci are being recombined and there are trillions of ways these loci can be passed from parent to offspring. We don't have the luxury to select for just the one allele you are looking at.  Being there are many genetic disorders out there in heterozygous and unexpressed forms (Ff) at individual loci combining them with themselves (line breeding or inbreeding will produce FF, Ff, and ff genotypes.  The reason it is not common for out-crossing to produce this problem is because it is not likely that two unrelated individuals carry the same disorder (recessive allele at the same loci).  It is very possible to fix a trait (dominant or recessive) into a line and not know it for several generations.  “Fixing” a trait into a line is a result of actually increasing the allelic frequency that causes the expression.  In-breeding through out a line repeatedly exposes the common “inbred” traits to others with the same “inbred” traits, and can fix a trait into a gene pool.  Therefore, when line-breeding or inbreeding, it is usually best to minimize the number of common dogs (dog of focus) you are inbreeding with in each line at any specific breeding.  Out-crosses maintain “hybrid vigor.” In-breeding an exceptional individual or line breeding off of a single exceptional individual is reasonable in order to increase consistency. However, being each common relative will carry some disorders, the more common individuals you have on both the top and bottom of a pedigree the more likely you are to have genetic disorders as well. Which is why I believe in/line-breeding is best done if only done by focusing on one common dog (who can be used multiple times if so desired) when possible. If you wish to inbreed down from more than one dog, I believe it is best to focus on one dog for at least 3 generations before in/line-breeding on another dog into the line in order to prevent unknowingly introducing recessive undesired traits within a line and not knowing where they came from. If one inbreeds down from two dogs at one time (as is done with full-sibling breedings that share both parents) you are likely to drastically compound the number of problems you will have…and you won’t be able to identify which grandparent is the problem. Although in some cases such a breeding may be highly desired, I don't believe it should be a common practice for this reason. Although a father-daughter or mother-son breedings are just as tight as are full-sibling breedings, they differ in the fact that they focus on a single individual (the one common parent), so when a strength or problem presents itself one knows the source. The more different dogs you inbreed in a line (upclose…within the last 3 or so generations) on both the top and bottom the more disorders you are going to have to deal with (in multiple mind you) while doing your selection…this makes your work more difficult. It is best to maintain the positive goals while minimizing the negative risks, which can be done my minimizing the inbreed individuals in a line you are working with.
 
By focusing on an individual you can have that parent both on the top and the bottom.  Half siblings (a good line breeding method with one common parent) or parent-child (if you wish to do a very tight breeding in-breeding) for example, only recombines the traits from this single specimen including the positives and negatives of a single specimen.  Being it should only be done with exceptional specimens, you are increasing the desired traits along with the unseen (most likely heterozygous) disorders of only a single dog.
 
by H. Lee Robinson, M.S. in Animal Sciences