Phenotype and Genotype

As researched and documented by Janet Lane © in various iterations over the (now many) years. Image: Waler mares Pearl, Topsy, Aria & Rigoletto at Clarkefield, Victoria

The Waler is a rare breed. The more we can learn and share what we know, the more secure their future will be. For the expert and the amateur alike, education is the most powerful tool available.

From the time Walers were actively bred, they were bred in the range situation, essentially as wild horses in huge areas of tough country. Since the days they ceased to be commercially bred many have continued to run as brumbies. We are most fortunate in this. It ensured the survival of good numbers during a time there was no one to take an interest in protecting them. They would be extinct otherwise.

And, contrary to what you often read in uninformed horse books, wild horses are the least inbred of any breed, and the healthiest. Nature precludes inbreeding through herd behaviour; with large numbers and vast unlimited range, our horses have enjoyed natural behaviour and good health to the max.

The immeasurable benefit has been the genotyping and phenotyping – the build of a strong horse; with the “unseen” traits of intelligence, frugality, endurance, athleticism. Due to survival of the fittest there’s a lack of hereditary faults, the genotype has beneficial dominants. This is complimented by the lack of inbreeding which gives a heterozygous gene structure (no over-dominants) so any fault or undesirable characteristic can be easily bred out. Most, if not all domestic breeds are homozygous – having a dominant gene structure – many of the dominants are undesirable. Many are over-dominant.

Originally bred from carefully selected breeds to deliberately create a type for a big market – the India trade – the Waler type once established, bred true. They have bred true for over a century and a half. Some people say Walers are only a type – a compliment. You need a type before you get a breed. The old rule of thumb was five generations breeding true meant a breed. Many breeds such as the Thoroughbred and Standardbred did not even have a type when they started their studbooks. Once a type breeds true for several generations, with no out-crossing to other breeds, then you have a breed; with most breeds, this is about the time studbooks start up.

Studbooks are not that old – many date from the twentieth century, some from the nineteenth century. With some breeds, records of breeding were kept, often sporadically, before their studbooks started although the breed was known and breeding true to type. Most breeds for which no studbook was formed became extinct. Some breeds, like the Friesian, Waler, Boerperd were brought back from the brink of extinction by starting a studbook, a long time after the breed was established. The reason many horse breeds became extinct was not only lack of a studbook, but lack of a use – with the invention of machinery, horses became redundant. Until people started to use them for recreation there was a time they were obsolete and unwanted. There was no market, so breeders could not keep going. It was the lucky ones with a breed Association – a protecting interest group – that got through these dark days.

Some stations went for heavy lines for the Artillery and domestic working horse market – there was no internal combustion engine in those days, horsepower was used for everything. Massive teams were needed for wool and wheat wagons – some had an 18-horse hitch. Other stations had the Trooper line, of which the greatest numbers were bred and sold; some had mostly Thoroughbreds (Officer types) as they also liked bush racing; others bred polo ponies. Many stations bred two or three types – all Walers, but of varying degrees of size and heaviness. They were run in separate mobs usually. A natural landform such as the McDonnell Ranges separated Troopers from Artilleries. Ponies liked it in the hills – in the bush the big horses are called “plains brumbies” and the ponies “rocks brumbies”. Sometimes from mustered mobs of the same area the horses were divided into “Wheeler” (heavy harness worker), “Leader” (more active harness horse) and “Trooper” (as we know them, weight-carrying remount) depending on heaviness and height, as they were drafted through the yards. These very descriptions were written alongside the colour, markings, gender and brands of horses off remount stations such as The Gardens, GoGo etc. Stations kept immaculate records of all stock sold. So, the various types we recognise came from deliberately bred horses. Look at the horse records from each of the foundation generation stations to see the different types of horses from each.

Genes are determined by the chromosomes, to which are attached alleles; we call this structure genes as they determine all seen and unseen things (traits) about an animal including us. A homozygous horse may have a few dominants, one or two for each trait, with three or four recessives. A Waler being heterozygous has up to twenty alleles for each trait, of which any random combination may become dominant in the particular animal. Alleles pair up to form a trait (gene) in the foal, alleles it inherited from both parents. If two identical alleles pair up, it’s homozygous for that trait, if two different alleles pair up, it’s heterozygous for that trait. Meaning, it has a dominant more likely to be passed on, or a dominant in that particular horse, but not so likely to be passed on. When you know identical alleles will pair up – dominants – or how they will combine with the very few recessives – it’s easy to predict what the foal will be like. There are very few possibilities. Most breeds can predict because they have artificially created dominants by inbreeding. Without relying on fixed dominants, there are many more possibilities. Coat colour, temperament, markings, conformation, and action. You also do not have fixed dominants for a fault.

The common way of fixing a dominant – making like alleles pair up – is by line breeding. This means breeding two horses together that have a common ancestor in the third generation, or further back. They are related, in fact. It’s a polite way of describing inbreeding that is not immediately close. Nevertheless, it is inbreeding, and with most breeds occurs over and over in pedigrees, so the horses in fact are inbred – related – for many generations. The genes “nick” that is, come together in a certain way, some alleles become dominant, a few become recessive, many disappear altogether. You can pretty well rely on this line-bred animal breeding true to type – others in its own likeness – it has less possibilities of doing otherwise. The problem is what if you didn’t get what you wanted? If you were breeding for speed but fixed in slowness? If you got the speed but also a crazy temperament? You’ve lost the chances of good temperament, or the chances of speed. Maybe you got the speed, but long cannons and sloping pasterns so the horse breaks down. Maybe it’s a bleeder. The horse will be dominant for all the good, and the bad things, you made dominant. You can’t get back the alleles you lost. It is difficult to lose inbred dominants.

Breeding any closer – inbreeding – say father to daughter, brother to sister, has even worse consequences. The genes radically alter: creating what are called “over-dominants”. The horse will throw the same as itself, faults and all, but the genes cannot be changed, as the other alleles are lost. It’s pure luck if you get every good trait and no bad ones, if not impossible. Many things crop up as a dominant with inbreeding, such as parrot mouth, undershot jaw, thin cannons, thin (not much hair) mane and tail, low intelligence and lack of common sense resulting in shying, crazy behaviour. These horses can damage themselves in a paddock, let alone in work. The alleles for normal mouth, wisdom, calm nature, good bone etc do not exist in the horse. It would take generations of outcrossing to a horse dominant for the good traits to try and rectify the damage – if you can find one in a breed that practices inbreeding. Throwbacks to the over-dominants will occur for generations.

The most inbred of modern breeds is the Arab with an inbreeding co-efficient of 39 percent – deliberate inbreeding and line-breeding has created this. Thoroughbreds are the next highest with 17 percent (bear in mind they are descended from just three stallions), line-breeding is common to try and get a successful nick for speed at all costs. The lowest inbreeding co-efficient is wild horses at 4.5 percent. Throwbacks are common with inbred breeds, Arabs in particular – cross out from an Arab three times (to another breed) and you may get a throwback utterly unlike what you expected, with most of the Arab traits; this classically happens in the third and fifth generation.

By maintaining a heterozygous gene structure, we maintain a good breed without relying on artificially fixing dominants – for our horses have few or no undesirable alleles, they are naturally dominant for good traits. The many alleles they have are not for extreme variations from the norm, but minor ones. Cowhocks for example were once required by Clydes; slight cowhocks still are by stockmen. Others may not want these. High action might be desired by some, not by others – neither however, affects the horses’ health. It may be hard to predict a foal colour. I’ve seen a brown and a bay Waler throw a chestnut, and two browns throw a chestnut. Two Walers with no white markings may throw a foal with four white feet and a blaze. There is a big range of colour and marking alleles – possibilities – that may become dominant in the particular horse. This is a type of “throwing back” – the foal may have the colour pattern of an ancestor. Throwbacks with Walers – meaning the unexpected dominance of previously unseen or unknown recessives – only affect traits with many recessives (possibilities) that are not harmful to the horse. They can randomly become dominants in the particular horse without affecting its well-being. Traits we know vary a lot but have never, as far as we can discover, come up with a harmful gene: such as colour, markings, action, and amount of feather. The genotype for essentials should not vary beyond benign and ideal: the stamp of a Waler stays true. The dominants and recessives in the vital areas are, virtually without exception, for strong build: good bone and tendon, hard well-formed hooves, good loins and rump, good chest and girth, upright neck carriage. And the attributes of bonding to humans, good nature, intelligence, frugality, and stamina. Any debilitating recessive becoming apparent, in any trait, is why we have classifiers – to weed this out. Problems are unlikely to occur, if so, only minor, and unlikely to breed on with a breed of strong natural dominants and equally good recessive variations fortified and perfected by ideal phenotyping.

How do you breed a certain line – the look, colour, build, behaviour, action of the type of Waler you want for your stud? The old-fashioned way, just as the early breeders did carefully for us. It takes about twenty years to get your stud type breeding true, the proper way. You select two parents with the traits you want, and breed them together, you hope the alleles dominant in those two, will match again to make a dominant in the foal. Once you get a foal that is exactly the type you want, you breed that (when it’s old enough!) to one just the same. None of these horses will be bred to any relations – no inbreeding, no line-breeding. You can, by breeding like to like, create a natural dominant for those features you want. If there is any problem, say for example one has popped up dominant for cowhocks – by breeding to a horse without cowhocks, you can immediately start making this recessive. By avoiding breeding to cowhocks, eventually you’ll make a dominant for good hocks. Problems are easily rectified, dominants are created naturally, and in a few generations, you’ll get your type breeding true. No problems fixed in. The way Walers were bred originally, and right up to now in the wild. Natural dominants have been established for good traits, those originally selected plus traits perfected by survival. We still have the many recessives – the things that will, until you fix them naturally, make coat colour, amount of feather, head shape, action, markings, slight conformation “faults” from the original breeds (once for a purpose, maybe not what you want though) still an occasional surprise packet. You can naturally fix these traits for dominants too, by selecting the ones you want and not breeding to those you don’t. It’s a true adage that it takes five generations (horse generations) to get your stud type perfect and breeding true to what you want. This is an almost lost skill. We have that very rare thing – a heterozygous breed. This should never change.

The outward appearance of the animal – caused by the particular way its genes are structured – what is dominant in that animal, what is recessive – is the result of its gene structure, and importantly, how that has been modified by the environment. The outward appearance is called the phenotype. The genotype is the genes that animal carries. You can’t see the actual genes, but you know what the dominants are in the animal for you can see its appearance, action, and nature, behaviour. You may know some of the recessives if you know its parentage and further back. Otherwise, you’re pretty much guessing – and unlike breeds with no or few recessives – we can guess all day and probably be right every time!

The Waler has a heterozygous genotype because the dominants are natural, not fixed (meaning losing a lot of recessives), and are not over-dominant (losing all recessives). To get an idea of the possibles in the genotype, you need to remember which breeds went into the Waler’s genesis – they had a head-start with excellent genotypes. Heavy horses, quiet horses, active horses, tough horses. The phenotyping (effect of environment on the genes) polished this genotype up, strengthened it and made it even better. The Waler has the best phenotyping anyone could hope for and then some. The harsh environment, numbers of horses, lack of human help and total dependence on its own survival skills have made the genes adapt and improve. Intelligence, adaptability, strength, never-say-die attitude, being foot-sure, stamina, bravery, caring for its own herd, powerful and correct conformation.

To show how phenotyping works: If you breed from a young Thoroughbred colt before he’s raced, and then again after he’s had a successful racing career, the foals are marginally different. The sire’s experiences have resulted in a little phenotyping (called commonly, “learning sperm”), making the later foal more likely to be fast, like the sire worked to be and became. If you leave a desert horse, say a brumby Waler, in highland snow country a season or two then breed, the foal will have a far better winter coat than its’ sire, or any foal he threw while in the desert – the phenotyping has hurriedly adjusted genes for a good winter coat. I have proved this with my little Waler stallion, and with two Waler mares. So, imagine many, many generations of phenotyping, where the environment has improved the genes and made a horse tough and wise and strong – the Waler. And how effectively phenotyping works on a breed without over-dominants that cannot change. What more could we ask in a genotype and phenotype? Ok, if they pooped money…

Of interest, a horse actually inherits one more chromosome from its dam than its sire – so the mother in fact contributes more to the foal’s genes. A good mare only should be bred from, the mare is marginally more important than the sire. The old adage – put the best to the best then hope for the best – is the way to go. The Arabs of the desert, the Bedouin many years back – at the time of the Walers campaigning there – knew the worth of good mares. They were far more highly valued than stallions. There’s an amazing account of some Australian soldiers capturing a grey Arab mare in WW1. Despite all attempts to disguise and hide her and taking her across Egypt, the Arabs tracked them down and stole her back. Her silver-mounted saddle is in the Perth museum. Had she been a stallion, they would not have bothered! The story is in the book The Great Ride, by Henry Bostock, published by Artlook Books, Perth. It’s the story of a Light Horseman in WW1, a top read.

Line breeding and inbreeding will lose the heterozygous gene structure. Mollycoddling our Walers will lose the phenotype. We must protect both. Running Walers in a big bush run is far preferable to small, neat paddocks where they do not have to find water, shelter, food. In a big run they learn to read wind direction and landform, find a warm place to camp, keep their teeth hardy eating tough plants, test the going, be careful with their feet. Listen and watch for danger and each other. They will get bored and cease thinking in manicured little fields. Their muscle and bone and tendon will not be needed and get finer. Teeth will get weaker. Their social structure and sense of care for their own kind will break down without natural herd behaviour. Colours, with rugs a constant protector, may wash out and more white appear, skin will get thinner, coats thinner, mane and tails fine. Faults won’t matter as much. Geldings obviously won’t breed on. But try to keep your breeding stock on a big run as much as possible. They won’t need you less – you still have carrots, lucerne, love. With Walers, visitors are always welcome! You can still bring them into the home paddock for some interaction, handling, and hand-feeding occasionally. Mares home to foal.

They are our legacy and we must see them right – the Waler as a strong wise horse, not a silly weakling wrapped in cotton-wool. If some stations can keep mobs going, or a reserve is set up that would be perfect. It’s difficult in our closed in, carved up world to find big runs and keep the Waler as it should be kept.

We can work with our limiting areas: do our best to prevent boredom, not overfeed, not over-rug, make sure exercise is taken and socialising with other horses takes place.

All the little things breeders do will make a big difference. Plant a few trees. Put feed as far as possible from water. Always have a salt lick. What’s the best shape for a horse paddock if it can’t be large? Is there a rubbing tree or post? A sand patch for rolling in? Ask someone if you can use a bush run now and then for your youngsters, and/or, your stallion and mares. You might meet someone interesting in the process. There’s nothing like being in the bush either. You might need a couple of mates to help move the horses, and muster them to bring back home – great fun.

Do what you can. You haven’t got a common horse in your paddock – you’ve got an extraordinary one. You aren’t just breeding for fun, you’re immensely improving the quality of horses available to the world. You’re the leader of your mob and need to keep the traits for which a Waler is famous. Best of all, doing all this is highly enjoyable – and Walers are very good at simply being enjoyed!

Posted by Janet Lane

Rare breeds advocate, and Waler researcher and owner/advocate since the 1980s.