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Each gene needs to be looked at individually and studied as to how it works when in combination with other genes. Each gene has a specific function but is partly or solely dependent upon all the others. We can now begin talking about how the terms are applied in understanding the combinations of genes and also some examples of genes that have combined and what colors they produce. 

     Every newborn puppy carries one allele at each Loci from each parent. If they carry two genes that are the same it is called Homozygous. If they carry two genes that are not the same it is called Heterozygous. Phenotype is what the dog's visual genetic makeup appears to be. Genotype is what the true genetic makeup of the dog is whether he visually shows the traits or not. Dominant genes produce the same phenotype whether they are paired with an identical or dissimilar gene. Recessive genes can be hidden or masked by a dominant gene.

    Knowing a little about the Loci and alleles we can go into further explanation with some of the terms using examples: Let’s take a black dog that is Homozygous for (AA). Meaning that it carries two genes of the same Allele at a Loci. When you breed that dog to another dog Homozygous for (AA) you will get a whole litter of black dogs. 

A dog that is Heterozygous, meaning that the genes at a specific Loci have two different allele; for example black (A) and tan (ay), when bred to another dog that is Heterozygous (A,ay) you will not only get black pups but also tan puppies (ayay)..  When an animal is heterozygous for a gene (Aay) and is black in color, the dog will visually express a phenotype of black, but as a genotype will be a black dog carrying a tan gene that does not show.

     A dogs genotype will not necessarily show all characteristics or traits that they truly carry. For example a tri colored dog that is showing the colors black-white-tan can carry as a genotype blue, but as a phenotype dog, it will visibly be seen as a black-white-tan color because the black-white-tan color gene dominated the blue characteristic. In order to see the presence of specific alleles it must be in a duplicate state. Otherwise a dominant one will mask it.
Below are some examples of formulas....

(AAbbDDspsp)=chocolate piebald 
(AABBDDeespsp)=lemon and white
(AABBDDspsp)=black and white
(AABBddspsp)=blue and white
(atatBBDDspsp)=black, white and tan
(atatBBDDSS)=black and tan
(atatbbDDspsp)=chocolate and white with tan points or chocolate tri, meaning 3 colors
(atatBBddspsp)=blue and white with tan points or blue tri, meaning 3 colors
(ayayBBDDspsp)=tan and white

        These examples are given with both alleles being the same at each loci. They would be considered as having the same genotype and phenotype because all the genes will show visually.

An example of a dog having a different genotype from its phenotype is:
(Aat BbDdspsp) this dog is visibly the color black. (A) black would dominate the (at) black and tan gene. Large (B) of black pigment would dominate (b) chocolate gene. This B) dominant gene would determine that the nose would be black not brown and the coat color would remain black and not turn chocolate because the (b) gene would need to be in double dose to override the black color.. Large (D) of full pigmentation would dominate (d) dilute and the dog would stay black and not turn blue. (spsp) would bring in the white Piebald color. This is a strong example of genes being hidden or masked by the dominant gene of the particular Series. 

The gene that is masked is known as a recessive and the color blue or chocolate is just that. A recessive gene does not necessarily mean there is something wrong with it or will produce defects. It simply means other genes can cover over it easily.

     If this dog, using the formula from above of (AatBbDdspsp) was bred to a chocolate or blue dog, some of the puppies would be chocolate or blue respectively because the recessive (b) or (d) would double up and appear in some pups when combined. It would look like this (AatbbDdspsp) or (AatBbddspsp).  The former being chocolate and the later being blue. There would be one more combination that could be produced with this mating and that is the color Weimaraner Gray also called Pearl in some breeds, with the formula of (Aatbbddspsp). In this instance both the (d) blue dilute and the (b) chocolate gene doubled up.

..........................HOW ALLELES COMBINE............................

     This section will start to explain how to combine the alleles within the 11 different Loci to come up with the combinations of genes that produce each coat color. But first a short review. One parent carries a series of genes which combine with the series of genes from the other parent. There are 11 different Loci (genes) which make up the formulas. To start we will discuss only four of the main genes which combine to produce a color. They are the (A), (B), (D), and (S) Series. Each gene plays a specific role in developing a color or pattern in the dog's coat. Once we learn how to combine the genes within each Loci, we can then learn to combine all the Loci together to get the resultant coat color formulas. 

  Let's say for example that the dam carries the genes (A at B b D d S si) and the sire carries (ay at B b D d sp sw). We need to combine these genes, in the (A Series) before we can combine them with the other Series. And so, we must combine the (B Series) separately and so forth through the entire chain of Loci. It looks like this:

Dam= AatBbDdSsicrossed or combined with the Sire=ayatBbDdspsw

What we've done is combines the Dam's (A) with the Sire's (ay) for the first combination (Aay), Then again the Dam's (A) gene is combined with the other (at) gene of the sire to get (Aat) the second combination. You then combine the Dam's other gene, (at) with again the Sire's (ay) gene to get the third combo of (atay), then lastly the Dam's (at) gene once again to the Sire's other gene (at) to get the fourth combination (atat). It may sound a bit confusing but really you just need to get the knack of it. The following drawing may help to clarify things.

Once this is accomplished, the separate Loci, already being combined, need to be combined with one another to arrive at a formula for producing the various coat colors. As an example of the formulas that can be produced, we will use a simpler combination of Loci and alleles::

Dam= AatBBDDSsp     crossed with    Sire=AatbbddSsp
First combine the separate Loci:

The Formulas Produced Are:
AABbDdSS= Solid Black
AABbDdSsp= Solid Black
AABbDdspS= Solid Black
AABbDdspsp= Black and white patches

AatBbDdSS= Solid Black
AatBbDdSsp= Solid Black
AatBbDdspS= Solid Black
AatBbDdspsp= Black and white patches

atABbDdSS= Solid Black
atABbDdSsp= Solid Black
atABbDdspS= Solid Black
atABbDdspsp= Black and white patches

atatBbDdSS= Solid Black and Tan
atatBbDdSsp= Solid Black and Tan
atatBbDdspS= Solid Black and Tan
atatBbDdspsp= Black and Tan with white patches.
 

You might say, there are many different formulas, how come the colors are coming out the same but the formulas are different? The reason is because genes are recessive and dominant. (A) is dominant to (at) therefore it will override the color (at) black and tan when it is seen in single dose. With a double dose of (at) the dog will be black and tan. 

(B) black or full color is dominant to (b) chocolate. A single dose of (B) will dominate the (b) chocolate coloration. (b) must be in double dose to produce the chocolate colors. Although each offspring will carry the (b) gene and can pass it on in future generations..

(D) is dominant to (d) dilute. (D) allows the black color to be retained with out diluting it to a blue color. (d) must be in double dose to dilute the coat to a different color. And so each offspring will carry the (d) gene and be able to pass it on in future generations..

(S) is dominant to (si), (sp), and (sw). It does not allow any white pigment to form on the coat therefore producing a solid color. (sp) in double dose makes the piebald pattern producing patches of color all over the coat. 

   As we can see, the separate Loci (ABDS) not only work with each other but also play specific roles in making up the overall color of the dog.  The rest of the Loci combine in the same fashion.

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