Wednesday, 4 January 2017

True F-crosses (Mendelian terminology)

The genetic terminology of filial generations (F) has been a bit misused on the web concerning breeding-back, and I am guilty of it as well. While I used an “F” for any crossbred generation, no matter which genotypic combination, it should only be used when F1, F2, F3… individuals are mated to each other respectively if you want to use that terminology in a genetically correct sense.
True F-cross products are interesting for breeding strategies because they are the most efficient way to fixate alleles in a more or less controlled way (while rampant cross combinations end up in genetic chaos) and to watch the Mendelian rules of inheritance (yes, most of the traits of a living organism are polygenetic, let us assume that for each of the single loci the Mendelian rules do apply). An F1 cross has one full set of chromosomes from one parental breed and one from the other. It has maximum heterozygosity that is possible between the two breeds, and is only homozygous for traits that are shared by the two breeds anyway. No matter how good the animal looks, how often you back-cross its offspring to it, it will not be able to increase the amount of homozygosity in the herd. Using an F1 bull for a long time can only spread the desired alleles in the population, but does not stabilize it. An individual that is half-pure does not have a chance of being homozygous for any of the desired traits except for those that are already shared by the parental breeds, no matter how good it looks.

Mating two F1 individuals to each other (they do not necessarily have to be siblings, but just be of the same genotype) would theoretically result in a continuum between the pure versions of the two breeds (how much offspring is necessary to see the full range of possible trait combinations depends on combinatorics).  
A true F2 individual has the chance to be homozygous for desired traits of both breeds, whereas a back-cross (B, in genetic nomenclature) with one of the founding breeds, no matter how good it works out, does not – a back-cross will be homozygous for many traits of the one breed, but for none of the desired ones of the other. Therefore, a back-cross is not a step forward, while using a true F2 for the next generations is more efficient than those of any combination, no matter how good they look.
In a postfrom 2015, I proposed the creation of a stable line using a breeding plan based on true F-matings. This concept has its practical challenges, and of course provokes inbreeding. Before I am going to cover the “true F” individuals I was able to find in the Lippeaue Taurus herd, I want to outline another topic where I think siblings matings played a role.

Large-horned Heck cattle

Heck cattle is extremely variable regarding horn size. I define horn size via two factors: a) horn length and b) thickness. Both factors vary from rather meagre to very large in this breed. Some Heck cattle actually have extremely large horns compared to most other breeds – in effect, looking only at the one end of the spectrum we see in Heck cattle, one would say this breed is one of the largest-horned breeds in the world. Just look at individuals like this, this or this. Why do some Heck cattle have that large horns? Readers familiar with this topic will know that the Wildgehege Neandertal, one of the most important Heck cattle breeding sites after World War II, used a half-Heck cattle half-Watussi cow in the 1950s for breeding. Because it was only one individual half a century ago, you barely recognize Watussi influence in modern Heck cattle (except for individuals like that for example, if you have an eye for it). But they kept on selecting for large horns, and therefore many of the Heck cattle of the Neandertal lineage have respectable horns. Still not that huge, however.
Walter Frisch, who had been breeding Heck cattle for more than two decades, probably created the Heck cattle lineage with the best horns in terms of aurochs-likeness (go here for more on this lineage). He consciously used inbreeding in order to stabilize desired traits (I assume that the focus was mainly on horns), including parent-offspring matings but of course also siblings matings.
Horn size, as a quantitative trait, is very likely based on many different gene loci that complement and/or summarize each other. The aurochs had a set of wildtype alleles on these loci that produced the horn dimensions it had. Domestic cattle most likely have mutations on these loci (some breeds perhaps only on some of them, others maybe on all) that either shrink horn size down in most cases, or in rare cases, augment it. I am not aware of any work on the genetic background of horn size, so my assumptions are just based on general basics – I’d be very grateful if someone discovered material on this topic and would direct it to me.
In any case, very large-horned breeds such as Watussi must have at least one or two alleles that cause those super-large horns. I cannot say whether these are wild type or not (the fact that their horns are larger than in the aurochs does not rule out that these alleles are wild type, f.e. if there were other loci whose wild type alleles normally counteract the super-growth of those horns that are mutated in the very large horned breeds). The fact that there are occasionally very large-horned Heck cattle with horns as thick as in Watussi implies to me that the alleles for such dimensions are probably recessive or incompletely dominant, otherwise there would be sequences of individuals which constantly display and pass on huge horns. Those alleles are probably floating around in the Neandertal and Wörth lineage heterozygously. Inbreeding, and especially siblings matings, probably lead to the more or less fixation of alleles for rather large horns in the Wörth lineage (though not completely, please read on) and occasionally even those that cause a very large-horned phenotype in Watussi become fixed homozygous in an individual. There are two examples in the former Wörth lineage that I know of: the bull Arturo and the cow Erni. Both are the result of siblings matings. In 2013, there was a Heck cow on the island which had rather small and thin horns, quite unlike the rest of the herd. Walter Frisch told me such individuals still pop out on occasion just like those with the oversized horns. It would be interesting to know if those very small horned members of the lineage are the result of siblings matings as well.

“True F” individuals in the Lippeaue population

Once again I take the Lippeaue population as my study subject. It is the herd I know best by far; I can trace down the identity and descent of almost all animals, and know what they look(ed) like thanks to stock lists and a photo archive I was provided by Margret Bunzel-Drüke and Matthias Scharf from the ABU. They use(d) only three to four breeds, what makes it comparably easy to comprehend the diversity of breed combinations and phenotypes. They have been breeding for more than twenty years now, what makes it the longest-lasting active cross-breeding project at the moment and therefore their herd has many of the possible combinations of the four founding breeds and some rather progressed individuals (the youngest individuals should be of the sixth cross generation by now). This alone makes the herd very insightful. And, furthermore, it is a very enjoyable fact that many of the Lippeaue Taurus cattle indeed look very satisfying.  
I would love to have the same opportunities with the TaurOs herds, especially as ever more and more cross combinations and grown crossbreed animals appear on the scene, but I have no personal contact to the TaurOs Project and therefore have limited possibilities on this project.

Using the material I have I searched for “true F” individuals of various genotypes in the Lippeaue population, also including animals that have been selected out or sold to other locations.

With the exception of Londo's, all photos are courtesy of Matthias Scharf, so please do not replicate without permission. 

Heck x Sayaguesa

A rather good Heck x Sayaguesa bull (Lucio) was used as a breeding bull on several sub-herds in the Lippeaue for many years, grazing alongside good cows like Lerida of the same combination. Consequently, there were a number of true F2 animals of that combination.

Leila, a daughter of Lucio and Locusta, was one of these. She seemingly looked quite good overall, although her horns were not satisfying in terms of curvature and volume. She left a number of descendants in the herd that are still present in the current population.
Lippe, a daughter of Lucio and Lerida, was quite good in terms of body and skull shape. She had (or has, she did not stay for long in the herd and I do not know her fate) a powerful shiny black coat colour, which is – although rather aesthetic to me – of course not desirable for a cow. What would be excusable if she had good horns, but for some reason she happened to have tiny horns that resemble those of Chianina a lot. This is surprising, as neither their founding Heck cattle nor Sayaguesa nor F1 crosses of that combination have such small horns. One explanation might be that both breeds have alleles that shrink down horn size but on different loci, and only F2 and subsequent combinations can be homozygous for both loci and display that small horn size. It is just a theoretic assumption as the genetic background of horn size apparently is not studied.
She did not leave descendants that I know of.
Loreley II was a fullblood sister of Lippe, but did not look that convincing (based on the photos I have), that is why I found her among the individuals that where selected out too. Her horns were not that good and she has no sexual dichromatism either, plus a white spot on the belly. The body shape and proportions look good, but she is rather young on the photos. She did not leave a track in the Lippeaue population.
Loreley II
Luxus was a fullblood brother of Leila. His trunk looks rather elongated on the photos, the head was short and the horns comparably small and not much inwards-curving. But his overall impression was not that bad as his colour was accurate, the body slim and the backline curved, so he was used as a breeding bull at Disselmersch (one of the sub-herds) for some time, and produced four descendants, of which none were kept for long.
Luxus; the other photos don't show this saddle
Lumumba was a son of Lucio and Lerida. It seems like he looked average, although his rump was rather heavy at the age of 2 already.

Heck x Chianina

I was unable to find true F2 for this combination. The reason for that is that the ABU only used one half-Chianina bull for breeding, Luca, at Hellinghauser Mersch, where there were no half-Chianina cows. A pity, it would have been interesting to see F2 of this combination.

(Heck x Chianina) x Sayaguesa

This combination seems to be the right mix to me – all three breeds are contained, and in an advantageous quantitative relation. This combination also includes all important aurochs traits. Note that counting this three-breed-combination as a genotype requires that these F1 are actually second-generation crosses, not first-generation. Lamarck, for example, is a second-generation cross bull but F1 for this genotype.

Londo is the best one of the true F2 I found for this combination. He is the son of Lamarck and 84 024, fullblood siblings. He resembles his father (which I is still one of my favourite Taurus bulls of all) a lot, has a curved back line, thick horns of an acceptable curvature and a correct colour. In contrast to his father, he has a chance of being homozygous for all these good traits, but unfortunately that also goes for the undesirable traits – he is smaller than his father and has a comparably longish trunk. Nevertheless, I still think this bull is qualitative because of its descent and looks, and it is currently used as a breeding bull at Klostermersch-Süd. Recently a male calf he produced with Larissa, the largest Taurus cow at the Lippeaue (more than 62% Chianina), was born – it has the potential to become a very useful future breeding bull.
42 621 is the daughter of Lamarck and Loxia. Loxia is/was a very good-looking cow, a full-blood sister of Lamarck. 42 621, however, did not work out well – diluted coat, short snout, horns that did not look promising. Genetics work by coincidence. Personally, I would have kept Loxia in the population, and in the same herd with Lamarck. This siblings couple had the potential for really good F2 individuals. I don’t know why Loxia was removed from the herd as she looked really good, perhaps her behaviour was un-suited or other reasons.
42 621
42 634 was the daughter of Lamarck and Laola, another quite good cow. 42 632 however, could have been better, as the horns were meagre, the colour had a slight greyish tint and the hips where higher than the shoulders. She was slaughtered because she was rather aggressive as well.
42 634
Her fullblood sister 79 808 worked out better in terms of body shape and also horns. Her colour is very faint as well, but in another way than in 42 621. While the coat of the latter was rather greyish, i.e. the amount of red pigment was reduced, 79 808 seems to have a reduced amount of black pigment, hence the beige colour like in Luca. So we are probably dealing with two different loci here. She was removed this year and left no descendants as she was (or is) quite young. Interestingly, her horns show the same kind of minor asymmetry that is also seen in Lamarck and some Heck cattle of the Wörth lineage.
79 808
79 844 is the only other F2 bull of this combination that I know of. Another son of Lamarck and Laola. He has a light colour saddle, but that saddle is not of such a faint colour that I would say it is the result of a dilution factor, it can also be a sign of lessened sexual dichromatism. But its face shows light markings that are typical for Chianina-influenced animals that show diluted colour variants. His body and head shape was not different from that of the other young bulls at Hellinghauser Mersch at this time (as far as I can tell), and its horns might have even become good or at least large, but its colour was obviously unsatisfying so he was removed in 2014 or 2015.
79 844
I have to conclude that Londo is the only really satisfying true F2 of that combination (despite its size) – well, genetics work by chance and five individuals are a small sample size. But these five individuals tell us interesting things about the parents. With the exception of Londo, all of Lamarcks’ F2 offspring have a more or less diluted coat. Lamarck himself is not diluted; it might be that his red pigmentation is reduced but it is not visible due to his solid black colour, but his eel stripe and forelocks show a powerful yellow-red colour, so I do not think so. Laola, 84 024 and Loxia definitely have a non-diluted wild type colour phenotype. So those factors that caused a faint or diluted colour in the F2 offspring must be recessive, and furthermore must be present heterozygously in both parents of the diluted offspring. And since the quality of the dilution is different between some of the animals, as outlined above, we might be dealing with two loci instead of one. While the cows must not necessarily have one allele for each of those two, Lamarck probably has one dilution allele on both of these two loci. That’s bad luck considering that the chance of him having one dilution allele from its Chianina grandparent is only 25% and that he is one of the phenotypically best Taurus bulls of all. But I think that does not dramatically decrease his value as a breeding bull at this stage, considering that those dilution alleles are probably widely distributed in the population anyway.

Lamarck has been moved from Hellinghauser Mersch to Klostermersch-Nord, where there are no cows of the same combination. But the new breeding bull at Hellinghauser Mersch, the huge 42 623, is of the same combination as Lamarck and so he can produce some more true F2 together with Laola and 84 024. From a genetic point of view, using more good F2 bulls should help progressing the herd – continuing to use half-pure bulls as breeding bulls will not effectively stabilize the population on long-term sight while a F2 as a chance of being homozygous for several desired loci of different founding breeds at the same time. The subsequent goal should be to achieve a good F3 bull by placing the F2 with cows of the same F-generation and genotype, which then is at least as or even more stable than its father, and to use this as a new breeding bull and so further. I think this could help to speed up the breeding process in a crossbreeding herd as progressed as the Lippeaue population currently is, more so than using half-pure bulls or than bulls of random combinations.