Non-Recognized Colors
Mismarked
Mismarked color is the most common discoloration pattern known in the Aussie and is most often shown as too much white on the head or the collar. It is not known for sure how mismarked color is transmitted, but the great variety seen in the Aussie must be due to modifier genes. Mismarked dogs are not normally affected by health problems, as seen in homozygote merles, but dogs with mostly white heads should be checked for hearing damage.
Diluted
This color is controlled by the D locus and is the most frequent non-recognized color to be seen among the Aussies, presumably because of the recessive inheritance. D is a so-called modifier, meaning that it alters the phenotype expressed by another gene. The recessive homozygous dog will have a diluted incorrect color, for example blacks become blue and reds, isabella. Diluted reds and especially red merles can be difficult to determine because the color can be mistaken for a pale, blurred red. Markings with tan are not affected. Diluted black is recognized in the Border Collie as being blue. One of the reasons why diluted isn´t recognized in the Aussie is perhaps because that, although the diluted black is beautiful, the diluted red is not wanted.
Diluted spots
Only merles have diluted spots. It is not known how it is transmitted but dogs that have them are more likely to transmit them and solid colored dogs can be carriers.
The two special colors, Tweed and Harlequin, are recognized by having several tones of the basic color, meaning spots with varied degrees of diluted colors. Both are transmitted dominantly and can be carried by solid colored dogs.
Running Copper
It is not known how running copper is transmitted, but it is most likely that some kind of modifier is involved.
White body splashes
White on the body can be caused by a simple elongation of the white markings, meaning modifiers that act on the si allele, as an expression of the sP allele as either a heterozygote or a homozygote, as the interaction of the H locus (Harlequin) on the M locus and as a result of breeding between two merles (MM).
Yellow
This color arises when the dog is homozygous for the recessive allele on the E locus. The E locus is responsible for the distribution of pigment in the hair, and when it is homozygous it prevents the distribution of color in the hair and turns the coat yellow. The dog is still capable of producing pigment on the skin which can be seen on the nose; a genetically black dog will have a black nose and vice versa. When ee is present it represses the expression of another gene from a different loci, meaning that ee prevents the distribution of pigment in the hair.
Yellow is recognized as a color in the Labrador retriever for example. One of the reasons why yellow isn't a recognized color in the Aussies is that it is impossible to see if the dog is a merle, and therefore the risk of breeding homozygous merles would be too high.
Sable
This color, which is popular in Collies, is not recognized as a color in the Aussies and is also very rarely seen. The color results from a hair with a dark colored tip, while the rest of the hair is much lighter. This color is controlled by the A locus (like tan markings) and the allele for sable is called ay. Sable is dominant to tan point, so a sable dog cannot have tan points. Sable also reacts with merle so a sable merle will have a muddy look.
Another related recessive allele is as. The homozygous dog will have black saddle-like markings like is seen on the German Shepherd. This color is also quite rare in Australian Shepherds.
-Credit: Anne-Lotte Prohl