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 is 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 article will largely be based on the fundamentals of gamete formation and recombination, and is meant to provide a simple understanding of the fundamentals of genetics; however, it should not be used exclusively to determine breeding pairs. By understanding these fundamentals, one is more likely 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 methods, but those that do not understand what is going on at a genetic level should study and learn as much as possible about both their dogs and genetics before actually breeding any animals. Line-breeding and inbreeding has its place within a breeding program when used properly. Unfortunately, many breeders fix genetics disorders within a gene pool as a result of inappropriately overusing these tactics due to a lack of understanding of what is actually occurring at the genetic level when one out-crosses, line-breeds, or inbreeds. Again, inbreeding can be highly effective when done correctly, but there is good reason why inbreeding is illegal among human populations, and that reason is because when done incorrectly it greatly proliferates genetic disease. My purpose for writing this article is to enable breeders that wish to learn the fundamentals of genetics a source to help them develop an understanding of some basics as well as to develop an understanding of when it is wise to out-cross, line-breed, or inbreed, and how to do so most effectively…to decide when to use each of these different types of breeding approaches within their breeding program, as well as how to do it in a manner that maximizes gains while minimizing risks.
Before we begin discussing how gamete formation and recombination occurs, lets go over a few terms…
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 (a specific address or location) within the genome (the entire set of nuclear DNA). 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 autosomal trait (traits that are not sex-linked), each parent donates one allele at each loci. I will come back to elaborate more on this later.
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 (less than 1% of the total DNA). 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. There are some sex-linked traits in dogs of course; however, they are something we seldom need to concern ourselves with unless there is a sex-linked genetic disease within a particular population of breeding stock. For this reason, 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 two alleles at each loci are needed to determine the proper 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; however, I will again repeat that this is very minor part of the total DNA (less than 1%), so I recommend not concerning yourself with mitochondrial DNA for now. "Don't throw the baby out with the bathwater" so to speak, meaning, it is foolish to ignore 99% of the DNA to chase 1%.
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 they contain 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 other polygenic (quantitative) 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 claim to understand the basic concept of dominance and recessive, but I have observed it is very common they actually confuse dominance with allelic frequency, which is a measure of how common an allele exists within the population, and is something completely different than actual dominance. Dominant traits does not mean common or normal. It simply means more powerful in its expression as it is an allele that is able to "mask" or cover up a recessive trait regardless of how common that recessive trait is in a population. Two individuals expressing a recessive trait (ex...light colored eyes) must be homozygous recessive (ex...aa) for that recessive phenotype to be expressed, and therefore recessive individuals cannot produce offspring with a dominant phenotype (ex...dark colored eyes) when bred to another recessive phenotype. Conversely, when an individual with a recessive phenotype is bred to an individual with a homozygous dominant genotype (AA) which shows the dominant phenotype (dark eyes), the resulting offspring will all be heterozygous (ex...Aa) but they will all display the a dominant phenotype (ex...dark eyes). Additionally, it should be noted that these heterozygous genotypes, despite all displaying the dominant phenotypes (dark eyes) can produce both the dominant and recessive phenotypes when bred to each other, as they carry both the dominant allele and a hidden recessive allele. This example can be easily illustrated with a simple Punnets' square. Now, replace the light colored eyes in the above example with a simple recessive monogenic disease, and we can see how inbreeding these individuals that appear normal can actually produce infected offspring. For this reason, it is again wise to study genetics before breeding. 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. When a heterozygous allelic combination is obtained in traits defined by dominance/recessive alleles, 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…
In this example, let's assume we are given a father that is homozygous for the favorable trait = DD (meaning he inherited an D from his mother and an D from his father). Let's also assume we are given a mother that is heterozygous for the favorable trait = Dd (meaning she inherited an D from one of her parents but an d from the other parent) DD x Dd…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 D the father donates, as his donation is simply a D no matter what; however, with the mother being heterozygous; the offspring can be either DD (if the mother donates a D) or Dd (if the mother donates a d).
A test cross is possible to determine if an individual was homozygous (DD) or heterozygous (Dd) within its genotype if the trait is controlled by complete dominance. To do this would require breeding to a recessive phenotype (which would have a genotype of dd). If your selected specimen for the desired trait was homozygous then crossing DD to dd would produce 100% offspring of Dd. Even though all would appear normal or dominant, all the offspring from such a breeding would carry the d allege. If the d allele is an undesired trait, you might think you would have a bunch of good pups as none would express the undesired trait, but in reality all of the offspring would carry the gene, and therefore if bred they could pass it on to their offspring. 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 (Dd) then breeding to a homozygous recessive (dd) would cause 50% to be Dd (carriers) and the other 50% to be dd 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.
It should be noted that just because a trait is recessive does not mean it is undesired. Some highly desired traits could be genetically recessive. While it is clear you can select for any given trait, we must also consider what is happening to all 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 (Dd) and unexpressed forms at individual loci combining them with themselves (line breeding or inbreeding will produce DD, Dd, and dd 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); however, out-crossing comes with its own risks, which include reducing consistency within a line as well as introducing new unknown genetic diseases that are not currently present in a particular line or family.
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 throughout a line repeatedly exposes the common “inbred” traits to others with the same “inbred” traits, which "fixes" (locks in) a trait into thee given gene pool. Therefore, when wanting to tighten up on a line, it may be best to limit the inbreeding in a program in order to minimize the number of common dogs (dog of focus) you are doubling up on, as each dog that is doubled up on increases the chances of hidden recessive issues being locked in and then later coming out...and can eventually create what appears to be a dead end to the line. Many great lines of dogs however are recognized as a combination of dogs that worked, and it is common practice to double up on several dogs at a time as a result, however, this can produce disastrous results, especially when one hasn't studied the line extensively.
Out-crosses maintain “hybrid vigor,” with vigor referring to healthy specimens that have genetic resistance to disease and overall seem to have good general fitness. 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. One of the reason an out-cross produces so well after many generations of inbreeding or line-breeding is because any issues that were caused by tightening up on a single individual or group of individuals in a gene pool are often immediately corrected by the out-cross. As a result, I believe it is best to not inbreeding or line-breeding on multiple dogs at the same time, and to limit the inbreeding or line-breeding focus on one dog for at least 3 generations before inbreeding or line-breeding on another dog into the line in order to prevent unknowingly introducing recessive undesired traits within a line unless one knows a line really well. The reason for this is because it is important to know where both the strengths and weaknesses within a line are coming from, and when one concentrates on multiple dogs at the same time it becomes difficult to isolate the source of any particular trait
To explain this, if one inbreeds down from two dogs at the same time (as is done with full-sibling breedings that share the same two parents) you are likely to drastically compound the number of problems you may have…and you won’t be able to identify which parent and/or 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, again unless one knows the bloodline really well. Meanwhile, father-daughter or mother-son breedings are just as tight as full-sibling breedings, but they differ in the fact that they focus on a single individual (the one common parent). Since the "parent-offspring" inbreeding only "doubles-up" on the parent (a single individual), the sources of identified strengths or weaknesses can be identified as they arise.
It is generally best to seek positive gains while minimizing the negative risks. By focusing on an individual every few generations you can minimize the risks while still having that individual on both on the top and the bottom of a pedigree. Additionally, half-sibling breedings can be a good method of line-breeding as it allows one to focus on a single one common individual as does the parent-offspring breeding, however, the these methods should only be done with exceptional specimens, as you are increasing both the desired traits along with the unseen (most likely heterozygous) disorders of only a single dog. Study your dogs and learn as much as you can about the traits of their ancestors before breeding.
H. Lee Robinson, M.S. in Animal Sciences
American Sentinel K9, LLC - Creator of the American Sentinel as the premier family K9 companion guardian. The American Sentinel is the most tested and proven bandog in existence today, and performs very well in protection dog applications or as a canine hunter (aka..."catch dog") of dangerous wild game, such as wild boar.
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