Border Collie Colors and Genetics

Basic Terms

Gene: A gene is like a set of instructions. They control pretty much everything about a creature; how it looks, grows, develops etc. Within color, genes tell the cells which type of pigment to produce.

Allele: Different variants of genes are called Alleles. They come in pairs and creatures inherit one from each parent. When writing about 'alleles' they are denoted as letters which each mean different things. 

Locus: All genes are tied together on long strands of DNA. Each point on this strand of DNA is called a Locus and is made up of the two alleles together forming a gene. The plural of locus is loci.

Series: The alleles at each locus are picked from a list of possible alleles which is called a series. Usually, there are 2 - 5 possible alleles that can be passed on, for example in the A locus there are 4 known alleles Ay, aw, at, a. Each locus has it's own series and the alleles in the series can only occur at that locus. Each dog will inherit a combination of the alleles possible. For example, some dogs will be "AyAy" or they could be "Ayat" or "atat". It relies on what their parents are and a little chance as to which of their parents alleles will be passed on.

Genotype: An animal's genetic makeup is it's genotype.

Phenotype: Phenotype describes what a creature looks like "on the outside". For example, the genotype of a sable dog is "Ay" and the phenotype of an "Ay" dog is sable. Not every gene in the dogs genotype will necessarily affect the dogs phenotype.

Dominant or Recessive: As stated, each dog inherits two alleles from their parents. Although every dog carries two alleles at each locus, only one of these alleles is generally expressed (meaning only one will actually be used, and the other will just effectively lie dormant). Which of the alleles is expressed depends on dominance. The most dominant allele will always be the one which is expressed in the phenotype. A recessive allele is one which is less dominant.
​Dominant alleles are generally written with a capital letter, for example B. Recessive alleles are written with a lower case letter, for example b. Sometimes there is more than one dominant or recessive allele on a locus. When this happens, there is usually an order of dominance, so one of the dominant alleles is more dominant than the other, and one of the recessive alleles is more recessive than the other. We generally talk of series having "top dominants" and "bottom recessives".
A dog with the BB genotype has two dominant alleles, and so it will only express B. A Bb dog will also express B because B is dominant over b. bb is the only genotype where the dog will express b.
It's also worth noting that sometimes both of the alleles on a locus will be expressed. This is called incomplete dominance (or co-dominance in some cases), and only happens on particular loci. The resulting dog will have a mixture of the two alleles, but its markings will generally lean more towards the more dominant allele. For example, the S series controls white markings, and the alleles in it display incomplete dominance over one another. The allele for piebald sp (white markings covering 50% or more of the body), and S is the allele for no white markings. A spsp dog will be piebald, but even though S is slightly more dominant than sp, an Ssp dog won't necessarily just be a solid color (as you would expect if a dog can only express its more dominant allele). Instead it may have some minimal white markings, because it is able to partly express it's more recessive allele (piebald).
Incomplete dominance and co-dominance are more-or-less the norm for most genes, however many of the dog color genes do happen to have a simple dominant/recessive relationship.

understanding The Loci That Make Up Color

In order of currently known dominance hierarchy. 

K Locus: There are three alleles on the K locus.
The K locus controls how the A locus is expressed.
KB - KB is solid. Nothing on the A locus can be expressed when KB is present, so no tan points or sable etc the dog will just be the base color (black, brown, lilac or blue). It's the most dominant on the K locus. That means that if the dog has one copy of KB the other allele on the K locus is not expressed.
Kbr - Kbr allows whatever is on the A locus to be expressed, but with brindle over it. So sable becomes brindle, and tan point becomes brindle point. Kbr is recessive to KB and dominant to ky.
ky - ky means that whatever is on the A locus can be expressed. So, sable, brindle, agouti or recessive black.

A Locus: There are four alleles on the A locus.
The A locus controls which genes produce eumelanin (Black, brown, blue, lilac).
ay - Ay is sable. The hair is tipped with the base colour but often looks red. Sable can hide merle as merle is only able to be expressed on eumelanin (black, brown, blue, lilac) and cannot be expressed on Pheomelanin (red such as clear sable or ee red).
aw - aw is agouti also known as "Wolf" sable and has banded hairs. It is very rarely (if at all) seen in border collies and is what typically marked German Shepherds look like. aw is recessive to ay but dominant to at and a.
at - at is tan point. It causes red or "tan" to be expressed at the points of the dog. Like Ticking, tan cannot generally be seen at birth, only under the tail, but develops quickly.
a - a is very rare and hardly ever seen in any breed, let alone Border Collies.

​B Locus: There are two alleles on the B locus.
The B locus controls whether a dog is black or brown.
B - B is black. It means the dog will have black fur, nose and eye rims.
b - b is brown. If a dog has two copies it means the dog will have brown fur, nose and eye rims.

D Locus: There are two alleles on the D locus.
The D locus controls whether a dog is non-dilute or dilute.
D - D is non-dilute. It means the coat will not be diluted to blue or lilac.
d - d is dilute. If a dog has two copies, it means the dog's base colour, black or brown, will be diluted to blue or lilac.

E locus: There are four alleles on the E locus.
The E locus controls which genes express phaeomelanin.
​Em - Em is masked. It means that if this gene is present the dog will have a mask of eumelanin.
Eg and Eh - Eg/Eh is grizzle/domino and is specific to Salukis. It looks a lot like shaded sable.
E - E is normal extension. This means the dog will express eumelanin (colour) and will be either black, brown, blue or lilac.
e - is recessive red or "ee red". This means the dog will express phaeomelanin (red) and be golden/yellow. The base colour will be seen through the nose and eye rims. Examples of ee include, white poodles, golden retrievers and samoyeds. The reason that some of these look practically white and some look gold is because of a theorised "Intensity locus" or "I locus"

M locus: There are five alleles on the M locus, though many are very newly discovered and cannot be tested through many conventional testing sites, these are also fairly rare.
M locus controls whether a dog will display the merle pattern over it's normal coat (normal eumelanin). Merle is an unstable gene and easily mutates into different lengths which will create a different look on the dog.
M - M is merle. The dog will have merle patterning over it's eumelanin.
Ma - Ma is atypical merle, a mutated merle allele with a different length. The dog will have an almost seal-like, dilute affected coat with few spots.
Mc - Mc is cryptic merle, a mutated merle allele with a different length. The dog will display little merleing but can mutate back to merle in it's puppies if the dog is bred. This should be treated like normal length merle.
Mh - Mh is harlequin merle, also known as herding harlequin. The normal merle patches are changed to white, much like in great danes.
m - m is non merle. This means there is no merle present.

S locus There are two known alleles and two theorised alleles on the S locus.
The S locus controls how much white a dog has. White hairs are when cells can't produce any pigment.
S - S is no white. All the cells are able to produce pigment.
sp - Sp is piebald. This means a dog will have lots of cells that are unable to produce pigment, particularly when they are homozygous Sp.
si - si is irish spotting, also known as the typical collar, white legs, tip of tail and blaze of white found in border collies. This gene is unidentified, and therefore untestable but it is theorised as most theorised si dogs breed "true" meaning all their offspring are also irish spotted and so on.
sw - sw is extreme white. It is theorised that this is responsible for extreme white such as english bull terriers but it is not known or identified. Most extreme white dogs test as spsp.

T locus There are three theorised alleles on the T locus. Their dominance hierarchy is unknown.
The T locus controls whether there will be spots of pigment on otherwise white sections.
T - T is ticking. These are small or large spots also referred to as "Naughty spots" and it is what's responsible for Dalmatian spots.
Tr - Tr is roaning. These are large clusters of spots and are what are responsible for Australian cattle dog like spots.
t - non ticking. This means that the dog has no pigment spots.

H Locus There are two alleles on the H locus.
Harlequin turns the dark grey patches of merle to white. This is different to Mh (although Mh does the same thing) as H harlequin, also known as "Dane Harlequin", has it's own locus and is inherited separately. So, a harlequin dog will be HhMm, but a dog could also be Hhmm and it not be expressed due to the absence of merle.
H - is Harlequin. The dog will have white patches where merle would've been if the dog is merle. If the dog is not merle then the harlequin will not be expressed but the dog will still be genetically harlequin.
h - is non-harlequin. The dog will be a regular merle if merle, if not merle it will not be genetically harlequin.

A note on Natural Bob Tail Natural Bob Tail (NBT) is a mutation in the T box gene where a dog is born without a tail. This does happen in border collies but is most common in Australian shepherds.
BT - is Bob Tail. This dog will be born with a shortened tail.
n - is not NBT. This dog will be born with a normal length tail.

Dangerous Colors and Patterns

There are a few patterns and colors that are dangerous or potential lethal in utero. This is why it is important to understand what you are dealing with when it comes to breeding, and why it is important for buyers to go to a responsible breeder who will test their dogs well and understand health, color and genetics.

​Merle: It is relatively commonly known that merle can be dangerous. This occurs when a dog is homozygous for the merle gene. This would be denoted with two capital M's - "MM" and is referred to as double merle. It's dangerous due to the fact that double merle dogs are often born lacking pigment, deaf, and/or blind. Merle must never be bred to another merle as there is a 25% chance per puppy of being a double merle. The dogs have these issues due to the fact hat the merle gene strips all pigment from the inner ear, meaning the dog cannot hear, and it causes the eyes to not develop properly in utero. Be aware, one copy of the merle, denoted as Mm will not cause any of these issues, only MM will and a responsible breeder will never breed two merles together.
Sable and Recessive Red (ee red): In and of themselves, sable and ee red are not dangerous, neither are sable or ee red merles. The issue with these two colours is that they are made of phaeomalanin and merle cannot be expressed over phaeomalanin. This makes the merle difficult to see and could end up with an uneducated breeder, breeding a merle to a merle through ignorance. Sable merles are easier as you can usually tell that a sable is merle at birth, with ee reds it is virtually impossible. It is therefore important that all sable merles are catalogued at birth and all ee reds are tested for merle using a genetic testing site and the recorded.
Extreme White Spotting/Piebald: High white dogs can be prone to deafness. This is due to the fact that the cells cannot produce pigment on the inner ear and therefore, the dog is deaf. Any born with two white ears should be tested for deafness through the vet.
Dane Harlequin: This is not something we have to worry about in border collies but it is interesting never the less. Homozygous harlequin, denoted as "HH" is lethal in utero. This means that any double harlequin conceived puppies will not live. They will either be reabsorbed by the mother whilst in utero or, occasionally, be born dead. This doesn't mean there can't be harlequin double merles but they would be simply "HhMM".
​Natural Bob Tail: NBT, similar to harlequin, is lethal in utero when homozygous, denoted as BT/BT. It is important to never breed two natural bob tails together in order to avoid this. 
Colour Dilute Alopecia (CDA): CDA results in dilute dogs who look vaguely mangey and suffer from hairless and skin problems. CDA is caused by d1, which is recessive to D (non dilute) but dominant to d - dilute. This means that it can be avoided through testing and could be bred out of all breeds through responsible breeding and testing for the faulty gene. Unfortunately, many breeders like the pretty colour and don't test for D1.

Merle Misconceptions (Ticking and Tweed)

Just a couple of misconceptions that  lot of people get confused on.
Often, a dog with ticking looks like it is merle. It is definitely not! It can be difficult to distinguish whether a dog is merle or not to the untrained eye, but usually it is pretty obvious. Ticking and roaning are merging spots that are black and muddle with the white spots to look grey. Merle is grey hair down to the root.

Another misconception is Tweed. Many people, who often unfortunately use an outdated website on Australian Shepherds, believe that for a dog to be tweed it needs 6 or more colours. This isn't the case, particularly in border collies, where it is believed that the dog needs to have a muddy patch bigger than a fifty pence piece.