Canine genetics - (this may take some time to read,

Canine Genetics…Things Every “Breeder” Should Know

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 millions of loci within a genome.

Loci – the location of a trait within the genome it 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 chromosomes. You have one set of 23 from your mother and another set of 23 from your father. These two sets combine to make up the 23 pairs of chromosomes, each pair being known as a homologous chromosome pair. The entire set of chromosomal pairs is known as the genome.

In canines, the number of chromosomal pairs is 39. Just as with one pair of shoes we would have two shoes total, when we have 39 pairs of chromosomes we have a total of 78 chromosomes in all. Of these 78 chromosomes, 39 (one set) again came from the mother and each chromosome paired with its partner from the chromosomal set obtained from the father.

The picture above is called a karyotype and illustrates these chromosomal pairs. For every trait, there are designated loci. It is the alleles at these loci that control the traits. 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 of the egg by the sperm, 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, in which the female “X” chromosome that comes from the mother does contain a small portion of information (relatively few traits) not found on the “Y” chromosome. Because sex-linked traits are not commonly known in dogs, I will not go into great detail of sex-linked traits at this time, but basically 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.

Another sex specific influence is mitochondrial DNA, which comes from the mother, but when discussing genetics I will not discuss this in further detail, as it is not found in the nucleus of the cell and is not in the chromosomes. For this reason, I don’t believe mitochondrial DNA is considered to be a portion of the genome, but only the mitochondria of the cells as passed down from the mother.

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 influencial 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 more difficult to select for.

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 millions of loci are being recombined and millions of loci are being passed from parent to offspring, not just the one 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 in-breeding will produce FF, Ff, and ff genotypes. The reason it isn’t 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 in-breeding, it is usually best to minimize the number of common dogs (dog of focus) you are inbreeding with on each line at any given time. Outcrosses maintains “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 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). 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 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, 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. This is done my minimizing the inbreed individuals in a line you are working with to a single individual per line. 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. When using full siblings you are recombining the disorders carried by both their parents, two different dogs. Line breeding down from two dogs has twice as many risks and with full-sibling breedings one doesn’t know which parent to credit and which to blame. For this reason, I do not promote full-sibling breedings.

Nice read so far. :) Just a few minor issues, which I would state differently. [quote="LeeRobinson"]Genome – The entire genetic code of an organism’s DNA. There are millions of loci within a genome. [..] millions of loci are being recombined and millions of loci are being passed from parent to offspring[/quote]

Well, it's not quite millions of loci, but rather tens of thousands. :wink: Still plenty when dealing with multifactorial traits.

[blockquote]Another sex specific influence is mitochondrial DNA, which comes from the mother, but when discussing genetics I will not discuss this in further detail, as it is not found in the nucleus of the cell and is not in the chromosomes. For this reason, I don’t believe mitochondrial DNA is considered to be a portion of the genome, but only the mitochondria of the cells as passed down from the mother.[/blockquote]

All true, but one should not underestimate the huge importance of mtDNA. For one, we're talking about the "power-factories" of the cell here - wouldn't that be kinda important in the context of stamina in working dogs? Moreover, as you already stated correctly, they are EXCLUSIVELY inhereted from the maternal side. This I believe could well serve as an eye-opener for many breeders, who solely rely on the quality of the sires. And lastly, let's not forget that mtDNA is of substantial interest in broader phylogenetics studies. Looking forward to part 2... :) Dan

Part I and Part II were combined in the post above. The title was made "Part I" when I posted it on a forum ( http://members5.boardhost.com/SSDA/ ) that wouldn't allow all the words in a single post. Thanks for the correction about there being tens of thousands of loci. When writing, I was in the mindset of "the endless possibilities" so to speak...but truthfully I was thinking of the combinations. And with many alleles choices for vast majority of the loci...and with quantitative traits...the possibilies of different outcomes are indeed "endless" as no two individuals besides identical twins are ever the same.

The reason I didn't go into mitochondial DNA any more than mentioned in my original post is simply because it isn't influenced by the father, but only the mother...and even then it isn't part of the "genome" so to speak being it isn't found in the chromosomes, and therefore isn't influenced by genetic principles. Being this was intended to be a post on genetics, mitochondial DNA wasn't intended to be my focus at this time...however, you are correct in the fact that the mitochondia do convert energy into a usuable form for the cell...and for this reason I have often thought that maternal mitochondia DNA may play a role in metabolism or stamina as well, but for me is speculation on my part as I don't know this to be an abolute fact and so I didn't comment on it further than is mentioned. Also, it is my opinion that the role of mitochondial DNA (that doesn't follow genetic principles) is far less significant than is the role of the entire genome (that does follow genetic principles)...but I am certain we both would agree much of this still remains to be learned. Simply put...knowing what we know today, there is no reason for breeders to remain so amazing clueless on how to put at least some of the basics of modern genetic knowledge into application...yet repeatedly I see breeders fumbling through the most elementary of concepts and doing it with error. Not long ago I heard someone foolishly claiming their dog was sired by two sires. :roll: (and that was a "reputable breeder"... :wink: )

It was observing repeated ignorance (I am not saying stupidity, but ingornance) that motivated me to post this message.