Genetic trait testing in dogs is remarkably complex due to gene interactions, but thankfully, many traits can be tested for, and now with MyDogDNA™ Advanced and Optimal Selection™ Canine Advanced’s Litter Predict, a breeder can plan matings to increase the chances of puppies with the looks they want. Below, you can learn about some of the common key trait interactions that produce a variety of unique, and sometimes unexpected traits.
Core Coat Colours
Two pigment families are considered the building blocks of coat colour: eumelanin, or dark pigments, and phaeomelanin, or red pigments. Three major loci or genes determine red and dark colour distribution in dogs: the Agouti (A) Locus, the Extension (E) Locus, and the Dominant Black (K) Locus. These genes are best considered together, as they interact with each other and serve as red or dark pigment “switches” at the level of the hair follicle. In turn, they are modified by other genes that influence the particular shade of dark or red pigment, or the absence of it.
Agouti – A Locus
What does the Agouti Locus do?
Agouti is both the name of the locus and the name of a pattern of red and black banded hairs typical of many wild animals. The Agouti locus houses the ASIP gene, which serves as a red pigment switch acting on the hair follicle, signaling it to stop making dark pigment and start making reddish pigment. The timing and location of this red pigment switching in the skin produces many interesting colour patterns.
Alleles in this group:
Agouti, Fawn, Tan Points, Recessive Black, Saddle Tan
Classic allele names: Aw, Ay, at, a, ST
Order of dominance:
Variants or alleles of a given gene or locus often have an order of priority; more dominant alleles are more likely to be expressed than recessive ones as they often need only one copy present to have an effect. From left to right, the order of dominance of the Agouti locus is:
Aw > Ay > at > a
A Locus interacts with:
Agouti alleles can be combined with modifiers such as Brindle, Red Intensity, Dilution, or Chocolate to produce interesting variations.
Agouti is hidden by:
Agouti Locus patterns can be hidden by Dominant Black (KB), which will hide all red coat patterns as solid black, and Recessive Red (ee), which will hide all Agouti patterns as solid red through a process called epistasis.
Extension – E Locus
What does the Extension Locus do?
The Extension (E) Locus affects the extent to which red pigment is displayed in the haircoat. The E locus houses the MC1R gene, which is a pigment regulator for the hair follicle, receiving signals to either produce dark or reddish pigment. Defects in the MC1R receptor result in exclusively red pigmented or white coats, regardless of A or K Locus alleles.
Alleles in this group:
No-Effect E, Mask, Widow's Peak (Discovered in the Afghan Hound and Saluki), Widow's Peak (Discovered in Ancient dogs), Sable (Discovered in the Cocker Spaniel), Recessive Red
Classic allele names: Em, E, EG, EA, EH, e1, e2, e3
Order of dominance:
From left to right, the order of dominance of the E Locus is:
Em > E > EG, EA, EH > e1, e2, e3
E Locus Interacts with:
Extension alleles can be combined with A locus patterns, or with modifiers such as Red Intensity, Dilution, or Chocolate to produce interesting variations.
Extension is hidden by:
E Locus patterns can be hidden by Dominant Black (KB), which will hide all red coat patterns except recessive red (ee). Some red coat patterns can be difficult to see in the presence of certain Agouti alleles.
Dominant Black – K Locus
What does the Dominant Black Locus do?
The Dominant Black (K) Locus affects whether red pigment can be displayed in the haircoat. The K locus houses the CBD103 gene, which acts at the hair follicle as a dark pigment switch. Dogs who inherit one or more copies of Dominant Black will be self-coloured or solid, and not show A or E Locus patterns, with the exception of clear red (ee). Brindle is a molecularly similar allele to Dominant Black and difficult to distinguish by most common testing methodologies, so it is reported as KB or Kbr. Brindle produces a “tiger striping” effect. No Effect Black allows A and E Locus patterns to be fully expressed.
Alleles in this group:
Dominant Black, Brindle, No-Effect ky
Classic allele names: KB, Kbr, ky
Order of dominance:
Brindle will not be visible if Dominant Black is present, as it is recessive to it, but will suppress No Effect Black. From left to right, the order of dominance of the K Locus is:
KB > Kbr > ky
K Locus Interacts with:
Brindle can be combined with A and E Locus patterns, or with modifiers such as Red Intensity. All K Locus alleles can be combined with Dilution or Chocolate to produce interesting variations.
K Locus is hidden by:
Two copies of clear red (ee) will hide the solid or pattern of K Locus alleles.
Coat Colour Modifiers
Coat Colour Modifiers affect the pigment shade, rather than the hair pigment type or pattern. Four loci or genes fall into this category: Brown (B), Dilution (D), Red Intensity (I) and Cocoa (Co) Loci. Brown, Dilution and Cocoa primarily modify dark pigments, and Red Intensity acts on red pigment. Some of these genes act by altering the pigment production pathway, others cause less pigment or clumped pigment to be deposited to produce a change in visible colour. Dark pigment modifiers affect all dark pigments throughout the body, including eye, nose, and paw pad colour.
Brown - B Locus
What does the Brown Locus do?
The Brown (B) Locus determines if brown or full black pigment can be expressed. The B locus houses the TYRP1 gene, which codes for a necessary enzyme to convert brown to black pigment. Mutations in the TYRP1 gene cause a defective enzyme which shortens the pigment pathway at brown, and thus all dark pigment throughout the body will be brown, including the nose, eyes, nails, and paw pads. Please note that in some breeds, brown pigment is referred to as “red”; here, it only refers to eumelanin pigments.
Alleles in this group:
Brown, Black
Classic allele names: B, ba, bc, bs, bd, basd
Inheritance:
Brown or chocolate (b) will not be expressed if a copy of B (non-chocolate) is present.
Brown alleles are equivalent and can be combined with each other, as long as both parents donate chocolate alleles. Notably, bd can be co-inherited (on the same half of the chromosome) from other b alleles, so if one parent donates two copies of chocolate, but the other donates B (non-chocolate), the dog will be able to produce black. Conversely, three or four copies of chocolate (b) may be present to produce a chocolate coat. From left to right, the order of dominance of the B Locus is:
B > ba, bc, bs, bd, basd
B Locus Interacts with:
Brown can be combined with any solid colours or A, E, or K patterns. B Locus alleles can be combined with Dilution to produce a unique colour called Isabella or lilac.
B Locus is hidden by:
Two copies of clear red (ee) will hide chocolate, but will typically still be evident in nose leather and eye colour unless white spotting is present.
Cocoa – Co Locus
What does the Cocoa Locus do?
Cocoa colouration is nearly exclusive to the French Bulldog, and is found in the HPS3 gene, affecting pigment production. All other known brown or chocolate variants in dogs are found in the TYRP1 or B Locus. Cocoa tends to cause a dark brown coat colouration and dark amber eyes, unlike B locus variants, which can produce lighter shades of brown.
Alleles in this group:
Cocoa, Non-Cocoa
Classic allele names: Co/wt, co
Inheritance:
Cocoa is a recessive allele (co), so two copies must be inherited to show the trait. The order of dominance of the Cocoa Locus is:
wt > co
Co Locus Interacts with:
Cocoa can be combined with any solid colours or A, E, or K patterns, much like chocolate or brown.
Co Locus is hidden by:
Two copies of clear red (ee) will hide cocoa although clear red is relatively uncommon in the French Bulldog. Cocoa will typically still be evident in nose leather and eye colour unless white spotting is present.
Dilution – D Locus
What does the Dilute Locus do?
Dilution variants are found in the MLPH gene, and cause clumping of pigment within the hair shaft. This results in sections of hair which are relatively transparent, giving the impression of a lighter colour. Eye and nose colour are also affected, with dilute dogs showing striking lighter-coloured or hazel eyes. Dark pigment (eumelanin) dilution is more noticeable, but red or yellow pigment (phaeomelanin) may appear “creamy” yellow. Three variants are currently tested for in Wisdom Panel™ breeder tests, but additional variants are likely to exist.
Alleles in this group:
Dilution, Full Colour
Classic allele names: D, d1, d2, d3
Inheritance:
Dilution (d) is recessive, so it will not appear unless two copies of dilution are inherited, one from each parent. Dilution alleles are equivalent and can be combined with each other. From left to right, the order of dominance of the D Locus is:
D > d1, d2, d3
D Locus Interacts with:
Dilution can be combined with any solid colours or A, E, or K patterns, and when Black and Dilution are combined, the colour is called blue or grey. In A or E locus patterns, the dark pigment is more impacted. D Locus alleles can be combined with Brown to produce a unique colour called Isabella or lilac.
D Locus is hidden by:
Dilution may not be readily evident in solid red (e/e) or predominantly red coats and in Merle (M) dogs, but nose leather and eye colour will typically show characteristic dilution.
White Spotting Patterns
White spotting in dog haircoats and skin is a regional lack of pigment, rather than a colour. Four loci or genes fall into this category: Piebald (SP), Merle (M), Roan (TR) and Harlequin (H) Loci. As pigment is necessary for normal hearing and eye development, caution should be taken when combining certain White Spotting Pattern alleles, as puppy health can be impacted.
Piebald - S Locus
What does the Piebald Locus do?
The Piebald or Spotting (S) Locus determines areas of absent pigment expression. The S locus houses the MITF gene, which governs the migration of pigment-producing cells during development of the skin. Piebald usually behaves in a semi-dominant manner, but recessive inheritance does occur depending on breed, suggesting complex inheritance pattern or expression. The distribution of the white spotting follows a general pattern, but additional unknown alleles may contribute to specific types, such as Irish trim pattern. Piebald alone or when combined with other pigment-inhibiting variants can increase the risk of deafness or abnormal eye development.
Alleles in this group:
White Spotting, Minimal White Spotting
Classic allele names: S, sP
Inheritance:
Piebald or particolouring often occurs with two copies (S/S) and white spotting with one (S/sP), but in some breeds, extreme white may occur with two copies of piebald. The order of dominance of the S Locus is:
S > sP
S Locus Interacts with:
Piebald and white spotting can be combined with any solid or pattern colour, hiding the red or dark pigment pattern of the coat. Ticking and roan patterns are only visible if white spotting is also present, and tricolour indicates the presence white spotting with a red and dark pigment pattern.
S Locus is hidden by:
Merle and albinism will hide or increase white spotting, as they also inhibit pigment expression. White spotting with merle or albinism increases risk of abnormal hearing and eye development.
Merle – M Locus
What does the Merle Locus do?
The Merle (M) Locus is an insertion of additional DNA to the Pmel17 gene, which is involved in pigment production. The merle pattern is different for each dog, as the tail length of the merle insertion varies as skin cells replicate during development. The longer the Merle length, the lighter the pigment produced by those skin cells, giving a patchy appearance to the colour of the coat. Merle predominantly affects dark pigments, resulting in black and silver coats, or chocolate and beige patterns. Red pigment changes are subtle. As with other pigment-interfering variants, merle and especially double merle can result in deafness and abnormal eye development.
Alleles in this group:
Merle, Non-Merle
Classic allele names: M, m
Inheritance:
Merle (M) is a dominant allele. Notably, inherited merle allele length (from mother and father) can vary, and some lengths produce little or no visible pigment interference and are less likely to cause deafness or eye abnormalities. Wisdom Panel™ breeder testing detects the presence or absence of merle and not the length. Additional testing is required to determine if the merle allele is standard (M), atypical (Ma), cryptic (Mc) or harlequin type (Mh). The order of dominance of the Merle locus is:
M (including Mh, Ma and Mc) > m
M Locus Interacts with:
Merle modifies any solid colours or A, E, or K patterns. M Locus alleles can be combined with Harlequin (H) to produce the Harlequin pattern of Great Danes.
M Locus is hidden by:
Merle patterning is hidden by white spotting and is difficult to discern in solid (e/e) or predominantly red coats (e.g. sable/fawn).
Coat Type and Other Coat Traits
Three genes interact to produce the majority of hair coat types and textures: the Long Hair (L) Locus, the Curl (C) Locus, and the Furnishings (F) locus. These three loci affect the hair growth cycle as well as the depth and angle of emergence of hairs. Hair thickness and coat density and genes governing wire coat are not known at this time.
Long Hair – L Locus
What does the Long Hair Locus do?
Long Hair is caused by variants in the FGF5 locus. To show a long coat, a dog must inherit two copies of a Long Hair variant, one from each parent. This can either be two copies of the same variant, or two of any combination of long hair variants. Some Long Hair variants are rare and relatively breed-specific, and some breeds’ long coat is not explained by these Long Hair alleles, such as in the Yorkshire Terrier. Other variants are suspected to influence coat length, and feathering may be an independent trait.
Alleles in this group:
Long coat, short coat
Classic allele names: L, l1, l2, l3, l4, l5
Inheritance:
Long coat is recessive, but all long coat alleles are equivalent to each other. The order of dominance of the Long Hair Locus is:
L > l1-l5
L Locus interacts with:
Long hair alleles can be combined with modifiers such as Curl (C) or Furnishings (F) to produce wavy or coats or furnished faces.
Long Hair is hidden by:
Long Hair can be hidden by Hairlessness through a process called epistasis.
Curl – C Locus
What does the Curl Locus do?
Curl is caused by a curved or angled hair follicle in relationship to the skin surface, with an oval opening on cross-section. Sometimes hair growth from the hair follicle is also asymmetrical. The Curl Locus is located in the KRT71 gene, involved in keratin production, the building blocks of hair and nails. Many curly-coated breeds produce multiple hairs per hair follicle, resulting in a very dense coat that is more resistant to cold, which may have contributed to the popularity of this trait in water-retrieving breeds. One additional variant of curly coat is known, but is not included in Wisdom Panel™ breeder testing, and additional variants may exist. Curly coats show reduced shedding, likely due to the shape of the hair follicles, and many curly-coated breeds require regular grooming for this reason.
Alleles in this group:
Curl, straight hair
Classic allele names: C, c
Inheritance:
Curl is semi-dominant, so one copy of curl (C/c) produces a wavy or ‘soft wire’ coat, and two copies (C/C) a tightly curled coat. The order of dominance of the Curl locus is:
C > c
C Locus interacts with:
Curl alleles can be combined with modifiers such as Long Hair (l/l), Short Hair (L/-), and Furnishings (F), and influence the appearance of coat patterns due to the coat texture. The Curl Locus is located close to the Furnishings Locus, so they often occur together.
Curl is hidden by:
Curl and wave are less apparent in short-haired dogs. Curl can be hidden by Hairlessness in a process called epistasis.
Furnishings – F Locus
What does the Furnishings Locus do?
Furnishings are the name for the elongated hairs of the muzzle and eyebrows found in certain breeds, and can be seen in dogs with long, short, straight, wiry or curly fur. Furnishings are caused by variants in the RSPO2 gene. The Furnishings often occur with Wire (gene unknown) and Curl (C).
Alleles in this group:
Furnishings, Smooth (non-Furnished)
Classic allele names: F, f
Inheritance:
The Furnishings variant (F) is dominant. Smooth-muzzled examples of otherwise furnished breeds do occur, e.g. Lhasa Apso, Portuguese Water Dog, as smooth (f) carriers are not visually distinguishable from homozygous furnished dogs (F/F). The order of dominance of the Furnishings Locus is:
F > f
F Locus interacts with:
Furnishing alleles can be combined with modifiers such as Long Hair (l/l), Short Hair (L/-), and Curl (C). Furnished dogs along with Reduced Shedding (sh) have markedly reduced shedding rates. The Furnishings Locus is located close to the Curl Locus, so they often occur together.
Furnishings are hidden by:
Furnishings Locus variants can be hidden by Curl (C) as the prolific coat hides the elongated hairs of the eyebrows and muzzle. Furnishings can be hidden by Hairlessness through a process called epistasis.
Body Features
Wisdom Panel™ dog breeder testing includes several tests for conformation traits, such as muzzle shape, ear carriage, and leg length, as well as some performance features, like high altitude adaptation. Most aspects of body structure and performance are complex in genetic inheritance, but more influential variants are sometimes known and available for testing. Below is a selection of the tests included for body features.
Head Shape
What contributes to head shape?
Head shape, including length and breadth of muzzle, amount of stop, plane of muzzle and skull, and shape of the skull dome are complex traits, governed by many genes. Two genes are included in testing that have been found to contribute significantly to muzzle length, SMOC2 and BMP3. SMOC2 accounts for about 36% of muzzle length variation. Effects of BMP3 have not been fully established.
It’s important to know that in many shortened-muzzle breeds, called brachycephalic breeds, these two genes are effectively “fixed,” meaning all dogs of those breeds will carry two copies of the variant. Additionally, effects of these variants on presence or severity of brachycephalic obstructive airway syndrome, or BOAS, have not been established.
Inheritance:
SMOC2 is a dominant variant, so any copies inherited will result in a shorter muzzle. In contrast, BMP3 is a recessive variant, so muzzle shortening or brachycephaly will only be observed if two copies are inherited. However, many other variants also contribute to head and muzzle shape.
Eye Colour
What causes eye colour?
Eye colour, or specifically the iris, is the result of pigment production, so final eye colour is a complex trait, dependent on several of the same coat colour modifier genes that affect coat colour and white spotting genes. In general, loss of pigment in the eye results in blue, green or hazel eyes. Brown eye shades can vary considerably, and the genes influencing shade are not yet known. Additionally, a gene called ALX4 is the cause of blue or bi-coloured eyes in Siberian Huskies and related breeds.
Inheritance:
Blue Eyes (Discovered in the Siberian Husky) are dominant (BLUE), and any copies of the variant increases the likelihood of one or two blue eyes. Additional genetic causes of blue eyes are known to exist, but no genetic testing has been developed.
Eye colour is affected by:
Final eye colour is affected by the presence of Chocolate (b/b), Dilution (d/d), Piebald (SP), Merle (M), Albinism (c), and Blue Eyes (BLUE). Chocolate often produces a light brown or yellow eye colour, while Chocolate with Dilution produces a unique pale hazel eye colour. White spotting, merle and Blue Eyes can produce partial or full blue eyes, and Albinism causes red or pale bluish eyes.
Ears
What affects ear characteristics?
Ear leather shape, size, set, and carriage are complex characteristics. The degree of stiffness of ear cartilage is a major determinant of ear carriage in part determined by the MSRB3 gene, which increases the likelihood of drop, rose, tipped or button ears when present. Ear leather size is also often increased if copies of CDDY, a variant that also causes short legs, is present.
Inheritance:
Variants or alleles of a given gene or locus often have an order of priority; more dominant alleles are more likely to be expressed than recessive ones as they often need only one copy present to have an effect. Floppy Ears are dominant (FLOP), and any copies of the variant increases the likelihood of non-prick ears. Ear shape, size and set are complex traits influenced by many variants and also environmental factors.
FLOP > prick
Ear carriage is affected by:
In addition to complex genetic factors that influence ear shape, size, and carriage, human interventions such as “training” of the ears into upright or folded shapes when young can affect the adult ear carriage of the dog.
Short Legs
What causes shortened legs?
There are several known genetic mutations which cause shortened stature in dogs. Most of the rare dwarfing variants included in Wisdom Panel™ breeder testing cause serious illness and are listed as disorders only, while two are listed under Traits, as they are purely cosmetic, or cosmetic with variable health risk. They can be inherited together or separately, and are very common in certain breeds.
The most widely-recognised short-leg variant is “breed-defining chondrodysplasia,” called Short Legs (Chondrodysplasia or CDPA), which causes significant limb shortening, and often, bowing of the legs. Dogs with 1 copy of CDPA are estimated to have 16-23% shorter legs, and 24-28% shorter legs if 2 copies are inherited.
The other variant that causes milder limb shortening, with variable risk of spinal disc disease, is Short Legs (Chondrodystrophy, CDDY). One copy of CDDY causes approximately 6% limb shortening, and 2 copies cause 10% - with very little twisting of the paired long bones, giving the impression of compactness, but not necessarily dwarfism.
Classic allele names: CDPA, CDDY, wt
Inheritance:
CDPA and CDDY contain the same sequence of DNA, but are inserted in different chromosomes. They can be thought of as semi-dominant traits, having an additive effect: the more copies inherited of either variant, the greater the limb shortening. Spinal disease risk is only associated with CDDY, and is dominant, meaning any copies inherited will increase risk, but risk of disc herniation varies considerably by breed. To learn more, please read “CDDY and Intervertebral Disc Disease in Dogs.”
Short Legs are hidden by:
In very small breeds, the growth-limiting effects of both CDPA and CDDY are not always visible, but will be evident in crosses with larger breeds in mixed-breed dogs. For example, the Chihuahua, Miniature and Toy Poodle, and Yorkshire terrier have been shown to carry short legs variants with high frequency. Additionally, the presence of the CDDY variant is not always evident in dogs that also inherit the CDPA variant, as the latter has a greater limb shortening and limb bowing effect. The breeds known to have the shortest legs, such as the Dachshund and Pembroke Welsh Corgi, typically carry two copies of both variants.
Final Thoughts
If you didn’t find the traits or trait answers you were looking for in this blog, please see the detailed information provided in your dogs’ individual traits results for more information about additional traits tested. Think your dog has a novel trait that needs research, or still have questions? Please reach out to our breeder customer service specialists at breeder@wisdompanel.com and we’d be happy to assist you!
