Genetics

APBT genetics PART II: Where oh where do all the genes go?
By Dr. Scot E. Dowd
I have not fully proofed this page but here it is:
I will come back and make it more reader friendly a little at a time.

This section of the genetic primer is essential for many reasons so I encourage you to really get into it. The main reason is I need to to dispel all visions of genetic simplicity that we portrayed in the previous section. This section will attempt to show you what you are really up against in regards to selective dog breeding.

In this and the next section, we will see why having a famous dog in the 3rd generation of your dogs pedigree may not mean anything in the world of segregation and crossovers (yep more terms and concepts).  You will find out why it means nothing to an educated breeder with knowledge of genetics to read advertisements for dogs that say “From GR CH bloodlines” rather than out of GR CHs. Stay tuned and you will find out all about the game of chance that is breeding. We will also discover why when you see a fabulous dog that is a great example of the breed and think to yourself “I want to breed this dog to my female” … those who know genetics will say “you should breed to that dogs sire instead”.  First however, we must take a step back and discuss issues related to inheritance. Our goal here is to introduce chromosomes and simplify the complexity (I love to simplify the complex) of segregation, independent assortment, cross-overs and random fertilization. This will lead to a discussion of randomization. To do this we will use the famous bead on a string imagery, which has the ability to aid us in visualizing the complexity of genetic inheritance.

CHROMOSOMES: WHAT ARE THEY REALLY?
Chromosomes: The figure below represents a typical cell like any cell in the dog’s body (except the gametes). Within the nucleus of the cell are chromosomes. As you remember the dog is a diploid organism that contains 39 “pairs” of chromosomes. A typical chromosome during division is composed of two chromatid connected by a centromere. We notice in the figure below that we have steadily unraveled this highly highly condensed molecule until toward the end (virtually magnified) we can visualize the individual base pairs of DNA. DNA by its chemical nature forms a structure called a double helix (don’t worry about this term but you can visualize a helix as similar to the coiling of a phone cord). This helix is capable of incredible condensations upon condensations as shown by the figure. There are three levels of condensation visualized here. The original DNA helix is wrapped around small proteins called histones. When wrapped tightly by the DNA the histones condense together in another helical shape which is even more condensed. This second helical structure composed of DNA and histones goes on to form another helical condensed structure that bunches up chemically and forms the chromatid.


Figure 2-1. This figure shows a Chromosome (with paired chromatid) that has been teased apart to help with visualization of how intricate and complex the chromosome actually is. I hope this image gives you a concept of how much information is contained within a single chromosome.  Below we will use the bead on string imagery. In this visualization we may consider a handful of genes as representing a chromosome in order to enhance or simplify our understanding. The reality is that each chromosome contains hundreds and thousands of genes. The genetics of reproduction has many many levels of intricacy that all introduce uncertainty even to the most knowledgeable breeder. Every piece of the puzzle you can put into place in your mind will help you breed better dogs. Image source: National Human Genome Research Institutes

With a basic knowledge of what a chromosome is we need to understand a few more principles that are highly influential in heredity.

GENES: We wear em but it is hard sometimes to find some that really fit well.
. If you remember our “BOOK” analogy from the previous segment. Genes are the sentences, codons the words, and DNA residues are the letters that make up the sentence. Here is where we begin to understand how genes interact to create the dog. First we have already preached that each of the chromosomes in the dogs cells has a non-identical twin pair (there is one chromosome that does not have a matched pair and this occurs only in the male dog, whose sex chromosomes or X and Y-chromosome do not have pairs. Males possess an X and a Y chromosome while females possess two X chromosomes but no Y chromosome).
Because there is a pairing of chromosomes each gene on the chromosome also has a pair (allele) located on it’s "twin" (paired) chromosome. Going back to our red nose black nose example. If we look at the F1 progeny that had the dominant B gene and the recessive b gene, one of these genes is contained on one chromosome (derived from one of the P parents) the second is contained on it’s paired chromosome (derived from the other P parent). One chromosome comes from one parent the paired chromosome comes from the other parent. Also note that the P generations (the line bred dogs) are BB or bb so have the same respective gene on each of the paired chromosomes.

Chromosomes are large scaffolds or frameworks that contain all of the genes. Genes are the information that dictate what characteristics the dog will possess. Genes are located along the length of the chromosome and are considered the basic units of inheritance.  One of the classic ways to view genes is called the beads on a string. In the figure 2-1 above you see the histones actually appear as small beads with the DNA coiling around them. In the beads on a string we use the string to represent the chromosome and the beads to represent individual genes. The figure below (2-2) represents a bead on a string representation of the two homologous chromosomes of a given dog. For the purposes of our discussion the green spots will represent non-type genes (undesirable genes) which we will also consider recessive. (Note: not all undesirable genes are recessive)

The sire of this dog (represented by the chromosome of figure 2-2) who is a champion has donated the top chromosome and the dam who is also a champion has contributed the bottom chromosome. One thing we notice is that none of the “bad” genes are paired with another bad gene. Because of this let us assume that this dog has all of the correct type for the breed and is also a champion. The second set of chromosomes however, is this dogs full sister (same champion mother and same champion father). This female has several serious faults because 2 of the major type genes are paired “bad”. How can this have happened? How can one puppy from a litter look perfect while the second puppy from the litter is a genetic mess. This is due to the law of dominance and the law of genetic segregation during the formation of the sperm and egg. Remember that with recessive genes, only when the recessive genes are paired (as are the i’s and n’s on the female from this litter) are we aware of their presence. The male has the same “bad” genes but they are phenotypically invisible. A familiarity with this simple double strand bead string will give us the key to the arrangement and the basic mechanism of heredity.

MALE FROM LITTER

FEMALE FROM SAME LITTER

Well, that was exciting and the visualization made a few pieces of the genetic puzzle drop into place I hope, but now we need to develop a solid understanding of what happens during the formation of sperm and egg (gametes). This discussion is vital and it is difficult for authors to develop in order for those with little practical knowledge of cellular biology can appreciate it, but please try and hang in there. I will eventually set up a forum where questions about these genetic pages can be asked and answered by myself, and others with such expertise. I will also say things in several different ways and use examples and graphics to reemphasize and better express the key issues.

The following table summarizes and reminds us of the meaning of the terms and concepts we have encountered. We must understand and even be conversant with these before going on as this vocabulary is the language we use to learn more important concepts. Just like it is hard to discuss Conformation of a dog without terms such as stifle and croup and zygomatic arch we cannot discuss genetics without terms like haploid and gametogenesis.

All of the dogs cells except for gametes are diploid (2n)
Eggs and sperm (gametes) are haploid (n)
Haploid (n)-- one set chromosomes
Diploid (2n)-- two sets chromosomes

The genome refers to the full compliment of chromosome pairs contained within each of the dog’s cells.

The genome of every dog is different

The genome within all of the cells of single dog are the same (except for gametes which are what??? haploid)

Sexual reproduction is the formation of new individual by a combination of two haploid sex cells (gametes).

Fertilization- (breeding) results in the combination of genetic information from egg and sperm that each have one half the original genetic information

Gametes for fertilization
Female- produces an egg
Male produces sperm
Both gametes are haploid, with a single set of chromosomes.
The new baby upon combining of the two sex cells is called a zygote. The two haploid sex cells combine producing two sets of chromosomes (diploid

GAMETOGENESIS: THE CORNERSTONE OF INHERITANCE
Gametogenesis (the generation of gametes) is the process where a full canine diploid genome (the 39 pairs of chromosome in the dog’s cells) ultimately creates haploid gametes (eggs and sperm). Later during sexual reproduction these haploid sperm and egg are united to create a new diploid dog. The term used to describe the cellular process that occurs during gametogenesis is Meiosis. The word Meiosis is Greek (if I remember correctly) and derived from meio, to make fewer, and osis, process. It results in the formation of cells containing one-half (called the Hapoid number) the number of Chromosomes (and therefore genes) of the parent cells. Remember that every chromosome has a pair (except the sex chromosomes of the male).
 Our ability to understand how a diploid organisms (dog) produces haploid sex cells which recombine to produce a diploid zygote (next generation dog) is vital to any future capacity we have to improve ourselves as breeders.

Gametogenesis is the process of forming gametes from diploid cells of the germ line (germ line IS the correct term here). The dog world tends to use the term bloodline synonymously).
In the male dog gametogenesis is appropriately called Spermatogenesis and is the forming of sperm cells by meiosis. This process occurs in specialized organs known as gonads (in males these are termed testes).  

In the female dog gametogenesis is termed Oogenesis, which is the process that results in the formation of ovum (egg) also by meiosis but this occurs in specialized gonads known as ovaries. One difference in this process is that spermatogenesis results in the formation of 4 functional sperm cells while Oogenesis results in the formation of one large egg and 3 polar bodies (polar bodies are eggs that do not develop).  Essentially all the energy of production during Oogenesis is concentrated in one cell at the sacrifice of the other 3. Male dogs produce hundreds of millions of sperm per day, while the female produces a dozen or so eggs each heat or menstrual cycle.
Spermatogenesis: In the figure below, the precursor cells (Germ cells) of the sperm or ova must multiply and at the same time reduce the number of chromosomes to one full set.  These germ cell lines thus duplicate each of the chromosome pairs. In the figure below each of the germ cell lines contains two pairs of chromosomes (as an example to illustrate this cellular process). In the dog cells instead of two we now know there are 39 pairs of chromosomes.

The germ cell lines form chromatids from each of the chromosomes by replicating the DNA. These chromatid represent the original chromosome and an exact copy of the chromosome joined together (refer to the figure of the chromosome at the top of the page) at the centromere. The cell is split and a pair of chromatid are pulled into each of these now haploid cells (secondary spermatocytes). Notice however that each of the chromatids contains two copies of the same chromosome joined at the center forming an X. The next step divides the cells again into four and each of the chromatids is pulled apart into separate cells. These Spermatid mature into actual sperm.

Oogenesis: The germ cell of the female follows the same process as the male sex cell. It duplicates its chromosomes so that the chromatid are joined. Then splits each of the X chromosomes into separate cells. There is a difference here however that makes the female of the species slightly more important from a genetic standpoint in many peoples opinion. One of the two cells from this division is basically turned off and does not develop. This cell can be seen attached to the larger cell. It is called a polar body. This polar body sacrifices itself to help the chosen cell mature. A second division also occurs where the joined chromatid are pulled into separate cells. During this second division when the maturing egg divides one of the divided cells is sacrificed and forms another polar body. The first polar body has also divided such that for every egg formed, 3 polar bodies are formed (sacrificed in a way) to help the chosen cell mature into an egg.



Figure 2-3 gametogenesis: This figure shows a schematic representation of sperm and egg production. The blue cells represent spermatogenesis while the yellow cells represent oogenesis. Notice that the first step creates paired chromatids in addition to the paired chromosomes. The paired chromosomes are then separated by cell division leaving a single chromosome with paired chromatid in each cell. These chromatid are then separated by a second cell division to produce 1 egg and 3 polar bodies or 4 sperm.

The end result from spermatogenesis and oogenesis is that the original diploid cell with a pair of each chromosome has been turned into 4 cells each with half this amount of DNA. Here is where we must really try and understand what is happening. Let us take another figure containing just beads on a string and follow each pair of chromosomes from two different dogs into the sex cells. 

In the figure below we have two dogs that are awesome champions. Each has a set of chromosomes where no bad traits are paired. Notice that the A chromosome in the male germ cell comes from this dogs sire and the B chromosome comes from this dogs dam. Similarly with the female germ cell (top cell), the C comes from this females sire and the D comes from this females dam. Follow closely gametogenesis as each of these chromosomes as they are duplicated to form paired chromatids and the cells divide. Ultimately, the final cells the chromatids are also divided and we end up with 4 sperm in the case of the male and 1 egg and 3 polar bodies in the case of the female. Thus from the original genome we have 2 A chromosome sperm and 2 B chromosome sperm out of the male (50:50). In the female as we progress through oogenesis we find that only the D chromosome ends up in the final mature egg. IT IS VERY IMPORTANT to realize that this segregation of chromosomes into the egg is a random selective process and it could easily have been the C chromosome that ended up in the final egg. Now what happens when we breed these two dogs together? There are only two possible combinations that can result. A sperm with an A chromosome can fertilize this egg or a sperm with a B chromosome can fertilize the egg. Isnt it interesting that no matter what combination (A/D) or (B/D) we end up with there is a doubling of faulty traits. What if the C chromosome from the female had ended up in the egg? In this case (A/C) and (B/C) both produce good pairing and we end up with a champion.



During the course of this discussion we have secretly introduced another concept and Menelian law known as Segregation. Segregation is a term that refers to the way the pairs of chromosomes in the germ-line are separated out into different sex cells during gametogenesis. Notice how the original A/B genotype of the male germ cell has been separated into 4 separate sperm cells? There are two more additive concepts that we must discuss related to segregation that will introduce you to just how complicated and unpredictable segregation makes breeding genetics.

Consider the dog genome with its 39 pairs of chromosomes. 39 of this dogs chromosomes come from it’s sire and 39 chromosomes come from it’s dam. When gametogenesis (which results in the formation of 4 haploid sperm or one haploid egg) occurs segregation can mix these pairs up completely so that (for instance) an egg can get 1 chromosome from the dogs sire and 38 from the dogs dam, or 5 from the dam and 34 from the sire, or or . or. There are so many different combinations that can occur during segregation it is near impossible to predict what gene combination related to which grandparent the eggs and sperm will get. This is one of the reasons we note that if you want to see what the puppies will be, look at the grandparents.

 Years past and even today when I talk or read what breeders have to say it is thought that a puppy gets 1/2 its genes from each of it’s 2 parents (This is true) and ¼ of it’s genes from each of it’s 4 grandparents (This is undeniably false). In fact we will see that it is definitely possible that a puppy may not get any genes from one of it’s grandparents. This is due to the law of independent assortment of homologues which combined with two other principles (recombination and independent fertilization) create almost an infinite number of genetic possibilities that can occur with any breeding.

The following 3 concepts are important because they display how infinitely complex breeding is.
I Independent Assortment of Homologues:

During the meiotic division of gametogenesis the homologous chromosome pairs
have random orientation

There is ultimately a 50-50 chance that resulting gametes will get maternal or paternal homologue of any given homologous pair. Remember in dogs their are 39 pairs.
Homologous chromosomes segregate randomly and independently without regard for maternal or paternal origins.

Number of combinations possible for gametes is 2n; where n is the haploid number of chromosomes.

In dogs the haploid number is 39

In other words it is possible that a bitch (or a stud) for instance could sort all of the genes from their sire into the egg/sperm. She could sort half of the genes from her sire and half from her dam. She could sort 1 of the chromosomes from her sire and the rest from her dam. OR ANY OTHER COMBINATION. In fact looking at the principles above the number of possible combinations of paternal chromosomes that could end up in the egg of a given bitch is 239 or 549,755,813,888 possible combinations. WOW HUH? What if the grand sire of your dog is GR CH ART and you got that 1 out of 550 billion chance that not one chromosome was segregated into the sperm that fertilized the egg that produced your puppy? YIKES HUH? There goes all that bragging.

This is also the reason why the brother of that awesome producer does not necessarily produce as well or the reason why the son of the great producer looks fabulous but does not produce even on par with his own quality. This is why a dog that is not the pick of the litter may outproduce a phenotypically superior sibling. This is why no matter how good of a breeder you think you are and how carefully you pick dogs you still can never REALLY know what you will get. This is why we call dog breeding the genetic game of chance. The odds may be that the grandson receives 25% of the grandsires germplasm but he could have received anywhere from one-half to NONE...and even then, did he get the better half? (see the bead on a string illustrations above).

Now let us complicate things further by adding yet another reproductive process that introduces even more uncertainty.

II. Crossing Over
Produces individual chromosomes that combine genes from maternal and paternal homologues
Occurs during prophase I at synapsis
synaptonemal complex
precise pairing
Sometimes homologous portions of two non-sister chromatids trade places in dogs (see figure below)
even two or three cross-overs per chromosome pair can occur


Above is an illustration providing a schematic example of crossing-over and recombination during the formation of gametes (germ cells) or meiosis. Here the original germ line with paired chromosomes (yellow and blue) form chromatids during gametogenesis. These chromatids can become “mixed together” resulting in an exchange of similar parts of the chromosomes. IN other words, during crossing-over chromatids break and may be reattached to a different yet homologous chromosome. This does not occur between non-paired chromosomes.  In this case the blue chromosome originally derived from one parent of this dog and the yellow from another. Thus, the final chromosome has a bit of both parents. This adds yet another complexity and uncertainty to breeding. Further increasing uncertainty.

In other words, during the early stages of cell division in meiosis, two chromosomes of a homologous pair may exchange segments in the manner shown above, producing genetic variations in germ cells. Thus, instead of producing only two types of chromosomes during gametogenesis in this case four different chromosomes are produced. This doubles the variability of gamete genotypes. The recombined inner alleles will align more with others of the same type (e.g. a with a, B with B).  Ultimately this crossing-over between homologous chromosomes produces chromosomes with new associations of genes and alleles.

III. Random Fertilization
FInally if both parents undergo independent assortment and no egg and no sperm are favored during fertilization (ie all sperm have the same chance to gain access to any given egg and any given egg has a chance of being produced and fertilized) then we can understand that fertilization is random. Thus we have added another variable to our chance at getting the perfect puppy.

Any one of 550 billion possible sperm cells (239) can, in theory, fertilize any of the 550 billion possible egg cells 550 billion x 550 billion = 302,231,454,903,657,293,676,544 possible puppies can arise from any given sire and dam. THis does not even account for cross-overs so if only 2 cross over events occur WOW the possibilities are truly limitless for the genotype of any puppy.
THIS IS WHY I LAUGH (INSIDE) WHEN I HEAR breeders MAKE BOLD STATEMENTS LIKE "I KNOW EXACTLY WHAT I WILL GET FROM THIS BREEDING" When you think about it that’s crazy huh?

Having said that let me also say
Don't get me wrong there are some breeders out there that know what they are doing to the extent that anyone really can. They have learned the principles involved in selective breeding and apply these principles logically and effectively.

 CLick on the link below to go to the new APBT genetics OF COLORATION PAGE
In the upcoming sections we will provide many things to help you on your road to breeding success; more terminology and principles especially related to gene interaction such as codominance, additive expression etc.
lists of canine genes and how they interact
the genetics of temperament and aggression.
the genetics of canine disease
OK OK since everyone is so infatuated with color I will describe canine color genetics (show you again why my red nose black nose example has problems)
We will then get into theory and practice in selective breeding including
principles of Linebreeding
principles of Outcrossing
principles of Inbreeding including inbreeding depression and why some breeders use inbreeding to find faults.
Backcrossing
Scatterbreeding