Thursday, 2 January 2014

Genetics of Cattle coat colours

First of all, a happy new year to my dear readers! 
Finally I had the time to write a rough introduction to the coat colours of cattle. Coat colour genetics are a very fascinating field and particularly interesting in breeding-back, because it is one of the very view qualitative features that are regulated by a low number of usually well-studied loci. That’s why coat colours change easiest in breeding.  My knowledge on coat colour genetics is superficial at best, therefore I apologize in advance for any technical errors that might be found in this text. I did this text mainly using T. A. Olson: The genetics of cattle: genetics of colour variation, 1999, and David M. Hillis of The Double Helix Ranch, as much as the very helpful work of two Carnivora Forum members.

Basic alleles

Although the more than 400 cattle breeds display an amazing variability in coat colours, the basic colour in taurine cattle is controlled by only 3 alleles on the Extension locus – E+, Ed and e. E+ is the wild type allele. Note that “wild type” does not mean that animals being homozygous for that allele automatically have the original colour of the aurochs with muzzle ring, dorsal stripe and sexual dichromatism; there are in fact many derivations of wild type colour. It means that the animals produce both eumelanin (black) and phaeomelanin (red) in various shades (in absence of dilutions), with head, neck, extremities and tail tips getting darker. The light muzzle ring and the dorsal stripe are often part of the expression of wild type colouring. A sure sign of wildtype colour are black nasal mucosa, dark tail tips and red calves that change in colour during their first months. Many cattle breeds are wild type-coloured, including Brown Swiss, Steppe cattle, Heck cattle, many Texas Longhorn and zebus, and of course all primitive breeds in Southern Europe and the Middle East. 
A bull with wild-type base colour (Braunvieh)
Ed is the “black allele” which results in a dominant solid black in both sexes and all ages. Galloways, Holstein-Frisian and black Highlands show this colour among others, but also many Lidia and Camargue. 

A black Highland
e is recessive under the two other alleles and results in a lack of black melanin, therefore wholly red animals. Highland cattle, Simmental, Fleckvieh and Red Angus display this colour. To avoid confusions (because aurochs-coloured cattle also show an optically red and black colour), when I call an animal “black” in this article, I refer to Ed, when I call it “red” or speak of a “red colour”, I refer to e.

Red Angus

There are three loci that have mutated alleles producing a dilution of coat colour, Agouti, Dilution and Dun. The Agouti locus for example. aw, white-bellied agouti, removes red pigment and a part of black pigment, it is present in Steppe cattle, Brown Swiss, Grauvieh, Heck cattle, Eastern European landraces and other cattle. ai is present in Steppe cattle and also Chianina, among others. As you can tell from their letters, both alleles are recessive. Abp, patterned blackish, intensifies the colour to almost black in both sexes. It is dominant relative to the wildtype. Ds, Simmental dilution, is responsible for the pale red colour of the Simmental and many Highlands. Dn, dun, is incompletely dominant and present in f.e. Brown Swiss and Chianina. Br is the locus for brindle; the brindle mutation is dominant over non-brindle and not visible in red animals (since they don’t produce black pigments).

Hungarian Gray cattle with a diluted coat
Interestingly, in the Manjampatti some rare Gaurs have a similarly diluted coat,
likely also caused by an Agouti mutation. They are not albinos, as erroneously stated on Wikipedia.
OT but interesting: The Charolais dilution is not present in any breed of interest here, but some Bisons have been or are still crossed with Charolais, and subsequent backcrossing with pure Bisons resulted in so-called white Bisons. Some people breed herds composed exclusively of these beautiful curiosities.


White spots were not present in the aurochs of course. Nonetheless it is important to have a look at these loci, because they are undoubtedly present in breeds used in breeding-back. Spotted breeds like the Hereford, Simmental, Holstein etc. have spots caused by the S locus, with Sp present in he Pinzgauer or Longhorn, which is dominant, and recessive s present in Holstein, Simmental and others. The Hereford pattern, Sh results in a white face, belly, feet and tail; it is incompletely dominant. The wildtype S+ produces no spots. Colour variants like Colour-sided, Roan and Belting are not relevant because no breed used up to date has these colours. The Blaze mutation results in a white head, leaving only a circular area around the eyes pigmented. It is incompletely dominant. According to Olson 1999, it is produced by the Hereford pattern. I suspect that it or a similar mutation might cause the circular pigmented areas in the otherwise grayish coat of many steppe-type cattle, but this is just a wild guess of mine.  

Sexual dichromatism

The prominent sexual dichromatism displayed by the aurochs and some primitive cattle is regulated by the amount of testosterone produced in the respective sex. The higher the testosterone level, the more eumelanin is produced and the blacker the individual will be. If an aurochs-coloured bull calf is castrated before getting dark-coloured, it will remain reddish-brown in colour. If a fully grown, optically black aurochs-coloured bull is castrated, it should redevelop a reddish coat again. Apparently the same is the case in the Banteng. Cis van Vuure reports a case of a male Java Banteng which got castrated and subsequently grew the red colour of a female conspecific.
Of course the amount of sexual dichromatism is heritable, so I guess the sex-based testosterone level has to be coded on one or more loci, but I haven’t read anything about that yet.

The Java Banteng shows a sexual dichromatism comparable to that of the aurochs 
Implications for breeding-back

In order to reduce the amount of undesired colour features, the founding breeds of an aurochs effigy breeds have to be chosen wisely. To put it in a nutshell, for the correct aurochs colour to be fixated in the population, the following alleles have to be present homozygous in all individuals (I’m not sure if the mutations on other loci are present on loci that arose completely new during domestication or if the have a respective wild type allele):

+ a well marked sexual dichromatism, whatever genes are involved to produce it.

All breeding-back attempts face similar problems regarding the coat colours: diluted colours, absent or weakly developed sexual dichromatism and white spots. Absent sexual dimorphism either shows in black cows, reddish bulls or both sexes displaying a colour something in between. Bulls with a so-called colour saddle are not desirable because evidence suggests that European aurochs bulls all were very dark brown to optically black with a light eel stripe. Nevertheless, bulls with saddles are common in breeding-back. The way I see it, the colour saddle in bulls can have two causes: either it is the result of a lessened sexual dichromatism, or of a dilution gene.

Heck cattle shows a high colour variability. Most individuals are wildtype coloured, although occasionally the recessive red colour appears, which was bred into the population by the use of Highland and possibly also Angeln cattle.

A red Heck cow
I don’t know if there are still Heck cattle displaying black, which was inherited by a bull of an old lineage of the Holstein (actual German name: schwarzbuntes Niederungsrind). Since it is dominant, it requires that there always were some totally black Heck cattle. Heck bulls with a saddle are quite common; in some cases it likely is the result of a weakened dichromatism, but many cases look like they are caused by dilution genes inherited from Gray cattle. Gray cattle was a very important founding breed of Heck cattle, and its dilution genes are still common is this breed. Braunvieh, another founding breed, contributed the recessive ai mutation as well. The Agouti mutations cause the animals to have a beige, tan or grayish colour, bulls to have a saddle. Dilluted cows often have that typical Steppe cattle-like “raccoon mask” with strongly pigmented circular areas around the eyes. Individuals being homozygous for those Agouti mutations are no rarity; their colour is not distinguishable from that of Gray cattle. UPDATE: Probably some Heck cattle also have the Simmental dilution Ds, because of Highland catt.e

Heck bull being homozygous for the Agouti dilutions inherited from Steppe cattle

A number of Heck cattle shows white spots. Since the only founding breed displaying white spots that we know of is the old Holstein, and modern Holsteins have the recessive s, I guess that the white spots in Heck cattle are recessive too. It produces white feet, a white tail and white spots on the belly, what is often seen in spotted Heck cattle. A white spot on the forehead is common among spotted Hecks as well. In Oostvaardersplassen, there are even individuals reported being completely spotted like Holstein (C. v. Vuure).
Spotted Heck bull in Oostvaardersplassen
A Heck bull calf with spotting which I photographed at
Lainzer Tiergarten, Vienna
Some Heck herds with no sexual dichromatism show a uniformly dirty dark brown to black coat. I wonder if that is the result of just a similar level of testosterone in both sexes or if it is in fact caused by the patterned blackish allele (Abp), which may have been inherited by the founding breed Braunvieh, since the Brown Swiss (a derivation of the Braunvieh) is said to have it according to Olson. 

Is this colour the result of absent sexual dimorphism or the patterned blackish allele?
(very ugly Hecks by the way)
Despite this number of undesired alleles, there are Heck herds with a very accurate aurochs colour, like the Hellabrunn herd in Munich which I already introduced in this post. It was the Corsicana that contributed the aurochs colour to the population, and the colour of the Murnau-Werdenfelser (another founding breed) isn’t that bad either, although its coat usually shows less eumelanin than it probably should. The Hecks from the Neandertal lineage used by the ABU to create Taurus cattle already showed a very good aurochs colour. Sayaguesa also has an advantageous colour because it has no dilution alleles. The very reduced or absent dichromatism is a disadvantage of course, but cows with a bull colour have been present in the population anyway. It is the Chianina that causes some “new old colour problems” because of its very reduced pigmentation. It has, just like Gray cattle, the recessive ai mutation plus the dun allele Dn, which is incompletely dominant. I presume that bulls with the dun allele get nearly always selected out because of their light colour, cows probably not that much; but I guess that the dun allele is less common in Taurus cattle than the agouti mutation, which is probably widely distributed in the population because it is recessive; just like it is in many usual Heck herds, so the selection work for a good colour done before with the Neandertal Hecks has to be repeated after the other features are stabilized in Taurus cattle. However, recessive features are extremely difficult to purge out effectively only by phenotypic selection (I’ll address that later on).

This Taurus bull (Heck x Chianina) shows the effect of one dun allele being present
Taurus cow being heterozygous for dun and homozygous for Agouti, based on
her ancestry and phenotype
Sayaguesa and also Lidia (and probably some other Iberian breeds) have one problematic colour allele though. Some Sayaguesa and Lidia show small white spots on the belly, probably the result of crossing with more derived breeds. Luckily they seem to be dominant, as I was told by Margret Bunzel-Drüke, and therefore should be easy to select out.

The Tauros Project will face exactly the same challenges in fixating a correct aurochs colour like Heck and Taurus cattle, since its founding breeds have all the same undesired features. Maremmana and Podolica have the Agouti mutations, but they usually are more pigmented and still retain a good sexual dimorphism. Some of their Sayaguesa and Sayaguesa x Tudanca cows display white spots on the belly. Highland cattle brings in black, red and brindle. Sayaguesa has a lessened dimorphism resulting in bull-coloured cows, Pajuna, Maremmana and also some Limia have a more or less prominent saddle and some Limia cows aren’t very strongly pigmented. If Barrosa is going to be used in the future as well, the problem of very lightly coloured bulls would be added. These deviant colours all have to be purged out by strict and effective selection; recessive alleles are most problematic because they are very difficult to clear off the population by mere phenotypic selection. It even gets increasingly difficult as the allele gets rarer, because its effects show up even less commonly. As far as I understand, the only efficient way to purge out recessive alleles is (unless you are hoping for luck) to screen the animals genetically for that allele and select out those who have it. Tauros Project claims that they will also select on a genetic basis in the future, but I don’t know if they are talking about this kind of genetic screening for recessive undesired alleles or something else. It is nebulous to me why they used red Highlands to cross them with their primitive cattle instead of exclusively black ones, as they bring in a recessive allele that would have been easily avoidable.

Brindled Tauros cow (Maremmana x Highland)
Having discussed the difficulties effigy breeding faces in fixating the correct European aurochs colour, I should not forget to point out that there is in fact cattle that displays a coat colour virtually identical to that of the aurochs. Primitive Maronesa herds for example, and very few Heck herds. In the past there also were herds of Corsican cattle displaying a very good aurochs colour, today there is probably no herd of this breed free of any colour mutations. Turkey, North Africa, and the middle east is also inhabited by a number of primitive breeds that yet have to be evaluated for breeding-back before they are replaced or outcrossed by more-derived cattle.

Aurochs-coloured bull in Kairo
Corsican cow with accurate aurochs colour

Note: My assumption that the “standard aurochs colour” was very similar over the range of the primigenius subspecies is based on artistic and historic references. There were no genetic evaluations of coat colours present within the aurochs populations using aDNA samples like in the case of the wild horse yet. Perhaps we might have a little surprise when such a study is done in the future that one or more colour alleles that were previously considered domestic were actually present in the aurochs as well, just like the case of the Leopard spotted complex in the wild horse.

Wait, what about zebus?

The wild type of the zebu, the Indian aurochs, is not known in historic references and there are no artistic depictions showing that subspecies for sure. But here is what I inferred for its fur colour based on parsimonious assumptions in this post:

The colour of the Eurasian aurochs displaying black bulls with an eel stripe and reddish or brownish cows and a mealy mouth in both sexes is also present in some Bantengs (except for the light eel stripe in bulls) and is indicated in some gaurs as well. It is even displayed by some primitive zebu cattle. Therefore the same basic colour must have been present in the wild Indian aurochs as well. The so-called “zebu tipping gene” causes a lightly coloured area between the legs cows and (some) bulls of zebus, and apparently the same gene is present in the Banteng, so the I. aurochs must have had it as well. The hair of the area between the horns is lightly-coloured in many primitive taurine cattle bulls and also in Gaur bulls, therefore some Aurochs populations must have had this feature. Because the same is found in some zebu, I apply it to namadicus as well.

Most zebu cattle are wild-type coloured, and diluted colours are very common. According to Olson 1999, these dilutions are caused by the Agouti and Dun locus, but it is not clear to me zebus have in fact the same mutations on this locus as taurine cattle. If this is the case, it is a likely scenario for me that these dilution alleles are a zebuine mutation that was transferred to taurine cattle by intermixing. Some zebu breeds show an undiluted aurochs colour, others have taurine black and red due to crossbreeding (it is possible however, that the aurochs colour is an artefact of crossing with taurine breeds as well). There are zebus, specifically Sanga cattle, that have somehow unique coat colours, and I think it might be possible that they are the result of zebuine Extension mutations that are not yet resolved. 

Gujarat Zebu with steppe cattle-like dilution
Weird Sanga cattle colour: e, E+, Ed or an unresolved zebuine mutation?

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