The Nature of Inheritance

Before we get into all the details about fun inherited traits, we need to understand how things are inherited. Let's talk about what each term is and what it means first.
DNA- This is the double helix you learned about in your science classes in school. If you aren't familiar, a double helix is much like a ladder that has been twisted over and over. Each "rung" on this ladder is made of a pair of molecules. We call this a base pair. These molecules are made up of alternating sugar and phosphate groups. Each molecule is one of four different bases: Adenine(A), Cytosine(C), Guanine(G), and Thymine(T). Adenine always bonds with Thymine and Cytosine always bonds with Guanine, hence why they are referred to as the base pairs. These pairs are sequenced in an order on the DNA strand, making a Gene per each segment.

Chromosome- This ladder of DNA is spun like a string on a spool. The "spool" is a protein called Histone. A full histone spool holds about 150 base pairs of DNA strand on it, and each segment of "full spool" is called a nucleosome. The nucleosomes bind together to create Chromatin fiber. The Chromatin fiber weaves together and this is what makes up a chromosome. In dogs, there are 39 different pairs of Chromosomes. So 39 from the mother, and 39 from the father. 
These particular details only matter when we are talking about what makes up the chromosomes. Now we'll be talking more about genes ON the chromosomes!

Gene- We look at the sequence of segments of the DNA strand on the chromosomes to determine gene traits. A select segment is referred to as a "gene". Each gene is responsible for a characteristic that has been inherited. Such as eye color, coat color and more. These are also in pairs. A pair of genes is always made up of one copy from the mother, and one copy from the father. Each gene has its set purpose and what traits are expressed. There are dominant and recessive genes, but we'll get to that later.
​Each gene has a determinate location on the DNA strand and we label each segment. This is what we refer to as a locus.

Locus- We refer to certain segments of genes as A Locus, B Locus and so on. The Locus that determines coat color will always be the Locus that determines coat color, but what determines the variation from dog to dog is called an Allele. 

Allele- We read the Locus to find the Allele variation. For example, when talking Aussies, we look at the B Locus to see what color the dog is. They can either be black or brown(though brown is often referred to as red). Alleles can also work in combination of each other to create different appearances on the dog. Let's say the dog is brown on the B Locus, and merle on the M Locus. So this is how we get Brown(red) Merle dogs. Everything we can read about the Alleles of the dog is what traits appear. 

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Okay, now that we've covered what these terms mean, now we can talk about inheritance! Inheritance is seemingly random, but it's actually a very calculated formula of likelihood. Remember how each dog has two sets of genes, one from each parent? Well each parent has their own set of genes, but the mother will only pass down one, and the father will only pass down one. So of the four genes between the two of them, there is a likelihood of inheritance. 
Let's just look at the B Locus for a second. Black is dominant and brown is recessive. We write black as a capital B, and brown as a lower case b. Since every dog has two copies of the gene, they can have two of the same OR two different alleles. So when a dog has a dominant allele, that is what will always be expressed visually. They can carry a recessive allele though and pass it on to their offspring. A dog with two recessive alleles will express the recessive trait.  A black dog with two copies of black is written as BB, while a Black dog that carries brown is written as Bb. A brown dog is written as bb, which is the recessive color. The easiest way to look at the likelihood of inheritance is by putting it in a Punnett square. The photo example below is a fantastic representation of this by UC Davis Genetic Laboratory. See how the two dogs used are both Black dogs, who carry brown.
By crossing these two together the following is possible:
A 25% chance of offspring coming out with two copies of the black gene, BB.
A 50% chance of offspring coming out with one copy of black, and one copy of brown, Bb.
A 25% chance of offspring coming out with two copies of the brown gene, bb.

We use this method to look at what our chances are in the offspring when we breed dogs. Every trait is calculated in this manner. In the Australian Shepherd breed, there are accepted colors/traits and unaccepted colors/traits in the breed standard. Aussies can come in many colors and patterns, but the only dogs that should ever be used for breeding is black and brown in solid or merle.
So now that you understand the nature of inheritance, we can look more at what colors and traits can be inherited in the Australian Shepherd breed!