Canine Genetics

Basic Genetic Concepts that 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 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 (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, 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 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.

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. 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…

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 a recessive phenotype (which would have a genotype of ff). If  your selected specimen for the desired trait was homozygous then  crossing FF to ff would produce 100% offspring of Ff. Even though all  would appear normal or dominant, all the offspring from such a breeding  would carry the f allege. If the f allele is an unfavored 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 (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. 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. 

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  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 focus on one  common dog 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...creating 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, which can produce  disastrous results. 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  outcross produces so well after many generations of inbreeding or  line-breeding is because any issues that were caused by tightening up in  a gene pool are corrected by the outcross.  As  a result, 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

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