The concept of natural selection is well known. Animals mate, animals are born, and those best suited to their environment survive to pass their genes on to the next generation. Populations, in time, improve their ability to cope with their environment.
A good breeding programme also improves an animal population over time. But this improvement is artificial, in that it is driven by people. And not with nature in mind, but with an end use for that animal in mind. Yes, nature still gets involved (eg deaths during birth, congenital problems, diseases, accidents), and breeders who go against the environment their animals live in do so at their peril. But ultimately it is the breeder, not nature, who selects which animals get to mate, and to whom. The breeder, not nature, decides who is and isn't suitable for breeding.
How a breeder does this is two-fold. The first is the selection process, deciding which animals get to pass their genes on to the next generation. The second is the actual mating process of matching selected males with selected females. We’ll cover these in the next two posts.
Having a breeding objective implies a desire to change an animal genetically. This in turn implies a need to improve an animal’s performance or productivity, as breeding is undertaken—or should be—with end users in mind.
But the end animal should also be considered. Its health, welfare and the system it is raised in all contribute to an end product and ultimately influence profitability.
Take dairy cattle. A cow in Africa may produce just over half a litre of milk a day, while in developed countries a cow can produce as much as 34 litres a day. This improvement has come from many generations of selecting for large udder size amongst other things. But how much larger can an udder get before a cow literally falls apart? Modern dairy cows already suffer complications from swollen udders, such as mastitis and lameness. Is continuing to breed for yet more milk production really the way to go? At what point is continual, linear, “improvement” no longer an improvement?
There is a phrase worth noting in any breeding programme: intermediate optimum. This is the value for a trait at which function or profitability is optimal.
A dairy cow may have optimal profitability with a “just right” udder size at which milk production, health and wellbeing are in equilibrium. Too small an udder, and production and profit drop. Too big, and health problems overwhelm production and profit.
An example of optimal function is hock set in animals, or the angle at the hock. Horses are especially prone to lameness if this angle is smaller or larger than the optimum. There is no valid reason to change this phenotype once the ideal angle is consistent amongst a breed.
Thus “improvement” doesn’t have to mean continual and linear change. “Improvement” instead could be the continual increase in uniformity across a breed by selecting for animals that meet optimum or near optimum performance for certain traits.
What is “best” will differ even amongst breeders of the same breed—as shown by the Border Collie example in that post. Two different breeders with two different—and valid— versions of “best”. Two very different breeding objectives, and yet the same objective: that of breeding an animal that “best” meets an end user’s needs.
Breeders should always keep the end user in mind when determining their breeding objectives. The end user, after all, is the one who will either buy (directly or indirectly) your animals or the products your animals produce. To know the end user is to know your breeding objectives.
Many breeding industries can be represented by a three-tiered pyramid. There are a small number of elite breeders at the top, who sell breeding stock to a larger group of breeders (or “multipliers”) below. Those breeders in turn build up numbers of quality animals to sell to a larger group again of end users below them.
End users in the sheep, cattle, pig and poultry industries are the commercial producers. They are breeders as well as producers, and seek animals that are reproductively and physically sound, and which will produce profitably and reliably the fibre, milk and meat demanded by processors and the public.
End users in the pet and recreational animal markets (dogs, cats, horses, birds, hamsters, snakes...) may never be breeders, but still have defined needs in mind. These could be performance (hunting dogs, race horses), aesthetic (beautiful, cute), or temperament traits (affectionate, protective), or any combination of these and other traits.
Going back to the pyramid model: ideally the end user would be the one driving breeding objectives. He knows what animals are best for him, and it is the multipliers above who are expected to supply those animals. They in turn would expect the elite breeders to supply the breeding stock that helps them meet those needs.
Sometimes though, breeding objectives become skewed and do not always have the end user in mind. For example, competition amongst the small group of elite breeders at the top of a commercial industry is strong. After decades or even more of breeding, all animals at that level are going to be of outstanding quality. It may be that at a prestigious show on which many future sales hinge, that a judge, in an effort to choose between two exceptional bulls, picks the one with the slightly more evenly spaced markings as there was nothing else that separated them. Suddenly coat pattern and colour—which do not increase productivity—have become important in an animal bred for milk or meat.
Your breeding programme must overcome such distractions and be focussed on your end users and their needs if it is to breed the best animal for that market.
Good breeders will have a breeding objective—a goal to develop an animal that to them is the “best” of its kind for the traits they desire. What is “best” for one breeder may well differ to what is “best” for another, and even for the same breed. For example, breeders of working Border Collies place importance on how well their dogs can herd sheep, and not so much on how they look. A breeder of show quality and pet Border Collies would place more emphasis on how symmetrical and evenly marked their dogs are. The objectives are different, but neither is more right than the other—each is “best” for the end purpose.
Most breeders would be familiar with the effects of environment on genotype. In Australia, temperate cattle breeds are found in the temperate regions and tropical cattle breeds are found in the tropical regions as this is where they perform best.
Yet not as many would be as familiar with genotype by environment interactions, and not knowing this concept may be detrimental to an oherwise sound breeding plan.
Going back to brisket disease in the Examples of Genotype-Environment Interactions in Animals post: let’s suppose a US cattleman with superior beef cattle but unfamiliar with brisket disease (extremely unlikely, but just to make a point!) relocated his herd from a low altitude to a high one. The consequences could be fatal for his herd and economically disastrous for him if his animals prove susceptible to high arterial pulmonary pressure. If he had never moved he'd have never known, and his valuable genetics would not be lost, though he may have always wondered why Colorado cattlemen never bought his prize bulls. (The test that measures pressure is only accurate above 1,800 m (6,000 ft).)
Several examples of G × E interactions are described in this document. The example on p2 describes research done on two closed lines of Hereford, a temperate beef breed. One line had been developed in Florida and the other in Montana. Some years later, part of each line was transferred to the other location, and each line evaluated side by side. The graph on that page (Figure 3) shows a noticeable difference in weaning weight, as well as a reranking of the two lines at each location. The Florida-bred line (genotype), though the same breed as the Montana-bred line (genotype), had adapted to the tropical environment of Florida and performed more consistently across the two environments. It outperformed the Montana line in Florida, but the Montana-adapted line still outperformed the Florida line in Montana. The graph is a real-life version of our hypothetical temperate-tropical graph from the Examples of Genotype-Environment Interactions in Animals post.
This example illustrates the point that breeders may—depending on their requirements—better meet their breeding objectives by sourcing new genetics from proven animals in their local region, rather than sourcing proven animals from very different environments. Similarly, breeders may not expect to sell animals—depending on buyers’ requirements—to environments different to the one they were bred in, and—depending on the traits—expect them to perform as well.
It is well worth considering in any breeding programme the potential effects of genotype-environment interactions. Being aware of such interactions may shed light on previous animal performance mysteries and help reach a breeding objective more effectively.
Remember that G × E interactions graph at least two genotypes and at least two environments. If just one genotype shows a change in different environments, the graph would consist of a single line. This represents nothing more than a simple environmental effect on animal performance, though of course it is just as important to consider in breeding plans.
It’s worth mentioning here that there are other graphable interactions involving genotype: genotype by management and genotype by economics.
A genotype by management interaction may show the best age for slaughter in terms of carcase weight and fat distribution for example.
A genotype by economics interaction might be apparent when considering labour and/or capital costs. Milk production is more productive with high input and labour than the reverse for example.
Genotypic interactions can be quite involved, but having an indepth knowledge of them can be very revealing and insightful. Ultimately a breeder can come to know a lot about The Animal is Part of a System and the industry itself as a system.
G × E interactions can occur between subspecies, breeds, and individuals within a breed. Let's cover an example from each.
G × E Interactions Between Subspecies of Bos taurus Genotypes: Bos taurus taurus and Bos taurus indicus Environments: Temperate and tropical
Bos taurus is the binomial (scientific) name for cattle. There are two subspecies of cattle: Bos taurus taurus (temperate cattle, eg the Angus and Hereford breeds) and Bos taurus indicus (tropical cattle, eg the Brahman and Afrikaner breeds). Photos of the many breeds within each subspecies can be found here.
The Bos taurus indicus subspecies is genetically adapted for tick resistance and extremes in temperature and humidity. The Bos taurus taurus subspecies is not, but is genetically adapted to cooler regions, and fattens readily on forage in preparation for cold winters.
The temperate subspecies performs better in temperate environments than the tropical subspecies, but the tropical one still performs well. In tropical environments however, the tropical subspecies outperforms the temperate one, though the heat, humidity and parasites are stressful conditions for both groups.
We could graph this interaction like this:
Note the reranking that occurs too.
G × E Interactions Between Breeds Genotypes: Brown Swiss, Jersey, Ayrshire, Guernsey and Holstein-Friesian dairy cow breeds Environments: High and low temperatures
High temperatures are well-known in the dairy industry to affect milk production. Australia has both temperate and tropical dairy breeds, but the temperate European breeds predominate in the industry. Summers in Australian temperate regions are hotter on average then Europe’s, so let us consider summer temperature variation in Australia as our E.
Of the popular temperate breeds in Australia, the Brown Swiss and Jersey cope best with heat stress, followed by the Ayrshire and the Guernsey, with the Holstein-Friesian coping least well of all. 
Please note that the following is not based on real data and is for illustrative purposes only. We might graph this interaction like this:
G × E Interactions Between Individuals Within a Breed Genotypes: High pulmonary arterial pressure and low pulmonary arterial pressure Environments: Altitude above and below 1.5 km (5,000 ft)
Brisket disease, or high mountain disease, affects cattle at altitudes above 1,500 m (5,000 ft) and has major economic costs in the USA.
The low oxygen content at high altitude causes the arterial walls in the lungs of susceptible animals to thicken, which decreases the diameter of, and increases blood pressure in, the pulmonary artery (the artery that carries deoxygenated blood from the right ventricle of the heart to the lungs). The heart has to work harder to pump this blood to the lungs, resulting in the right ventricle enlarging. Eventually the right ventricle becomes so enlarged that it cannot contract any more. Fluid may leak out through the blood vessels and into the brisket and up into the neck and jaw, and/or across into the belly. The animal is lethargic and eventually dies from lack of blood flow to vital organs. Alternatively the animal dies more quickly from heart failure when the buildup of pressure becomes so great that the right ventricle’s valves blow out.
The disease can be selected against by only using bulls with low pulmonary arterial pressure, which is a reliable and heritable measure against the disease.
Because the disease only manifests at high altitudes, we might graph this G × E interaction like this:
The next post will cover how knowledge of G × E interactions can help develop suitable breeding objectives.